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1395 lines
54 KiB
TeX
1395 lines
54 KiB
TeX
%
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% $Id$
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%
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\label{sec:nwARGOS}
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%\newcommand{\mc}[3]{\multicolumn{#1}{#2}{#3}}
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\newcommand{\mc}[3]{\mbox{\bf #3}}
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\newcommand{\vb}[1]{\mbox{\verb.#1.}}
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\newcommand{\none}{\multicolumn{2}{|c|}{ }}
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%%%%%%%\renewcommand{\thetable}{\Roman{table}}
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\newcommand{\mcc}[1]{\multicolumn{2}{c}{#1}}
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\def\bmu{\mbox{\boldmath $\mu$}}
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\def\bE{\mbox{\bf E}}
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\def\br{\mbox{\bf r}}
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\def\tT{\tilde{T}}
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\def\t{\tilde{1}}
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\def\ip{i\prime}
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\def\jp{j\prime}
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\def\ipp{i\prime\prime}
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\def\jpp{j\prime\prime}
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\def\etal{{\sl et al.}}
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\def\nwchem{{\bf NWChem}}
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\def\nwargos{{\bf nwargos}}
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\def\prepare{{\bf prepare}}
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\def\nwtop{{\bf nwtop}}
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\def\nwrst{{\bf nwrst}}
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\def\nwsgm{{\bf nwsgm}}
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\def\argos{{\bf ARGOS}}
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\section{Introduction}
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\subsection{Spacial decomposition}
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The molecular dynamics module of \nwchem\ uses a distribution of data
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based on a spacial decomposition of the molecular system, offering
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an efficient parallel implementation in terms of both memory
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requirements and communication costs, especially for simulations of
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large molecular systems.
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Inter-processor communication using the global array tools and the
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design of a data structure allowing distribution based on spacial
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decomposition are the key elements in taking advantage of
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the distribution of memory requirements and computational work with
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minimal communication.
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In the spacial decomposition approach, the physical simulation
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volume is divided into rectangular boxes, each of which is
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assigned to a processor. Depending on the conditions of the
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calculation and the number of available processors, each processor
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contains one or more of these spacially grouped boxes.
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The most important aspects of this decomposition are the dependence
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of the box sizes and communication cost on the number of processors
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and the shape of the boxes, the frequent reassignment of atoms to
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boxes leading to a fluctuating number of atoms per box, and the
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locality of communication which is the main reason for the efficiency
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of this approach for very large molecular systems.
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To improve efficiency, molecular systems are broken up into separately
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treated solvent and solute parts. Solvent molecules are assigned to
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the domains according to their center of geometry and are always owned
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by a one node. This avoids solvent--solvent bonded interactions
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crossing node boundaries. Solute molecules are broken up into
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segments, with each segment assigned to a processor based on its
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center of geometry. This limits the number of solute bonded
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interactions that cross node boundaries. The processor to which a
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particular box is assigned is responsible for the calculation of all
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interactions between atoms within that box. For the calculation of
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forces and energies in which atoms in boxes assigned to different
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processors are involved, data are exchanged between processors. The
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number of neighboring boxes is determined by the size and shape of the
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boxes and the range of interaction. The data exchange that takes place
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every simulation time step represents the main communication
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requirements. Consequently, one of the main efforts is to design
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algorithms and data structures to minimize the cost of this
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communication. However, for very large molecular systems, memory
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requirements also need to be taken into account.
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To compromise between these requirements exchange of data is performed
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in successive point to point communications rather than using the
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shift algorithm which reduces the number of communication calls
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for the same amount of communicated data.
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For inhomogeneous systems, the computational load of evaluating
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atomic interactions will generally differ between box pairs.
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This will lead to load imbalance between processors.
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Two algorithms have been implemented that allow for dynamically
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balancing the workload of each processor.
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One method is the dynamic resizing of boxes such that boxes gradually
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become smaller on the busiest node, thereby reducing the computational
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load of that node. Disadvantages of this method are that the
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efficiency depends on the solute distribution in the simulation volume
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and the redistribution of work depends on the number of nodes which
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could lead to results that depend on the number of nodes used.
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The second method is based on the dynamic redistribution of intra-node
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box-box interactions. This method represents a more coarse load
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balancing scheme, but does not have the disadvantages of the box
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resizing algorithm. For most molecular systems the box pair
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redistribution is the more efficient and preferred method.
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The description of a molecular system consists of static and dynamic
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information. The static information does not change during a
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simulation and includes items such as connectivity, excluded and third
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neighbor lists, equilibrium values and force constants for all
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bonded and non-bonded interactions. The static information is called
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the topology of the molecular system, and is kept on a separate
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topology file. The dynamic information includes coordinates and
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velocities for all atoms in the molecular system, and is kept in a
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so-called restart file.
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The \nwchem\ molecular dynamics module is the parallel implementation
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of the vectorized code \argos\ developed at the University of Houston.
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\subsection{Topology}
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\label{sec:nwatopology}
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The static information about a molecular system that is needed for
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a molecular simulation is provided to the simulation module in a
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topology file.
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Items in this file include, among many other things,
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a list of atoms, their non-bonded parameters for van der Waals and
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electrostatic interactions, and the complete connectivity in terms
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of bonds, angles and dihedrals.
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In molecular systems, a distinction is made between
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{\it solvent} and {\it solute}, which are treated separately.
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A solvent molecule is defined only once in the topology file,
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even though many solvent molecules usually are included in the
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actual molecular system. In the current implementation only one
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solvent can be defined. Everything that is not solvent in the
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molecular system is solute. Each solute atom in the system must
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be explicitly defined in the topology.
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Molecules are defined in terms of one or more {\it segment}s.
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Typically, repetitive parts of a molecule are each defined as a single
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segment, such as the amino acid residues in a protein.
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Segments can be quite complicated to define and are, therefore,
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collected in a set of database files.
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The definition of a molecular system in terms of segments is a
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{\it sequence}.
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Topology files are created using the \prepare\ module.
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\subsection{Files}
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\label{sec:nwafilenames}
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File names used have the form \verb+$system$_$calc$.$ext$+, with
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exception of the topology file (Section \ref{sec:nwatopology}), which is named
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\verb+$system$.top+.
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Anything that refers to the definition of the chemical system can be used
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for \verb+$system$+, as long as no periods or underlines are used.
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The identifier \verb+$calc$+ can be anything that refers to the type of
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calculation to be performed for the system with the topology defined.
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This file naming convention allows for the creation of a single
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topology file \verb+$system$.top+ that can be used for a number of
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different calculations, each identified with a different \verb+$calc$+.
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For example, if {\tt crown.top} is the name of the topology file for
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a crown ether, {\tt crown\_em}, {\tt crown\_md}, {\tt crown\_ti} could
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be used with appropriate extensions for the filenames for energy
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minimization, molecular dynamics simulation and multi-configuration
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thermodynamic integration, respectively. All of these calculations
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would use the same topology file {\tt crown.top}.
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\label{sec:nwaextensions}
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The extensions \verb+<ext>+ identify the kind of information on a file,
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and are pre-determined.
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\begin{table}[htbp]
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\begin{center}
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\begin{tabular}{ll}
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{\bf acf} & free energy correlation data file\\
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{\bf cnv} & free energy convergence file\\
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{\bf coo} & coordinate trajectory file\\
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{\bf day} & dayfile\\
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{\bf dbg} & debug file\\
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{\bf dre} & distance restraints file\\
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{\bf emt} & minimization trajectory file\\
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{\bf fet} & free energy step contribution file\\
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{\bf frg} & fragment file\\
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{\bf gib} & free energy data file\\
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{\bf mri} & free energy multiple run input file\\
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{\bf mro} & free energy multiple run output file\\
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{\bf nw} & \nwchem\ input file\\
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{\bf nwout} & \nwchem\ output file\\
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{\bf out} & molecular dynamics output file\\
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{\bf pdb} & PDB formatted coordinate file\\
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{\bf prp} & property file\\
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{\bf qrs} & quenched restart file, resulting from an energy minimization\\
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{\bf rdf} & radial distribution function output file\\
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{\bf rdi} & radial distribution function input file\\
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{\bf rst} & restart file, used to start or restart a simulation \\
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{\bf seq} & sequence file, describing the system in segments\\
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{\bf sco} & solute coordinate trajectory file\\
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{\bf sgm} & segment file, describing segments\\
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{\bf slv} & solvent coordinate file\\
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{\bf svl} & solute velocity trajectory file\\
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{\bf syn} & synchronization time file\\
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{\bf tst} & test file\\
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{\bf tim} & timing analysis file\\
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{\bf top} & topology file, contains the static description of a system\\
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{\bf vel} & velocity trajectory file\\
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\end{tabular}
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\end{center}
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\caption{List of file extensions for nwchem chemical system files.}
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\end{table}
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\subsection{Databases}
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Database file used by the \prepare\ module are found in directories
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with name \verb+$ffield$_$level$+, \\
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where \verb+$ffield$+ is any of the
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supported force fields (Section \ref{sec:nwaforcefields}).
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The source of the data is identified by \verb+$level$+, and can be
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\begin{center}
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\begin{tabular}{lll}
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\hline
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level & Description & Availability \\
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{\bf s} & original published data & public \\
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{\bf x} & additional published data & public \\
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{\bf q} & contributed data & public \\
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{\bf u} & user preferred data & private \\
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{\bf t} & user defined temporary data & private \\
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\hline
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\end{tabular}
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\end{center}
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Typically, only the level {\bf s} and {\bf x} databases are publicly
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available.
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The user is responsible for the private level {\bf u} and {\bf t}
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database files. When the \prepare\ module scans the databases, the priority
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is {\bf t}$>${\bf u}$>${\bf x}$>${\bf s}$>$.
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The extension \verb+<ext>+ defines the type of database file within each
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database directory.
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\begin{table}[htbp]
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\begin{center}
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\begin{tabular}{ll}
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{\bf frg} & fragments\\
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{\bf par} & parameters\\
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{\bf seq} & sequences\\
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{\bf sgm} & segments\\
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\end{tabular}
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\end{center}
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\caption{List of database file extensions.}
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\end{table}
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The paths of the different database directories should be defined in a file
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{\tt .nwchemrc} in a user's home directory, and provides the user the
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option to select which database files are scanned.
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\subsection{Force fields}
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\label{sec:nwaforcefields}
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Force fields recognized are
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\begin{center}
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\begin{tabular}{ll}
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\hline
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Keyword & Force field \\
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{\tt amber} & AMBER95 \\
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{\tt charmm} & CHARMM \\
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%{\tt cvff} & CVFF \\
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%{\tt gromos} & GROMOS87 \\
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%{\tt oplsa} & OPLS/AMBER3.0 \\
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%{\tt oplsg} & OPLS/GROMOS87 \\
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\hline
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\end{tabular}
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\end{center}
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\section{Format of fragment files}
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Fragment files contain the basic information needed to specify all
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interactions that need to be considered in a molecular simulation.
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The format of the fragment files is described in Table \ref{tbl:nwafrag}.
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Normally these files are created by the \prepare\ module. Manual
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editing is needed when, for example, the \prepare\ module could not
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complete atom typing, or when modified charges are required.
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\begin{table}[htbp]
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\begin{center}
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\begin{tabular}{p{15mm}p{12mm}l}
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\hline\hline
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Card & Format & Description \\ \hline
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I-1-1 & a1 & \$ and \# for comments that describe the fragment \\ % $ for emacs
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\hline
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I-2-1 & i5 & number of atoms in the fragment\\
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I-2-2 & i5 & number of parameter sets\\
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I-2-3 & i5 & default parameter set\\
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I-2-4 & i5 & number of z-matrix definition\\
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\hline
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\mc{3}{l}{For each atom one deck II} \\
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\hline
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II-1-1 & i5 & atom sequence number \\
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II-1-2 & a6 & atom name \\
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II-1-3 & a5 & atom type \\
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II-1-4 & a1 & dynamics type\\
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& & \verb+ + : normal\\
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& & \verb+D+ : dummy atom\\
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& & \verb+S+ : solute interactions only\\
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& & \verb+Q+ : quantum atom\\
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& & other : intramolecular solute interactions only\\
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II-1-5 & i5 & link number\\
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& & 0: no link\\
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& & 1: first atom in chain\\
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& & 2: second atom in chain\\
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& & 3 and up: other links\\
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II-1-6 & i5 & environment type\\
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& & 0: no special identifier\\
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& & 1: planar, using improper torsion\\
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& & 2: tetrahedral, using improper torsion\\
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& & 3: tetrahedral, using improper torsion\\
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& & 4: atom in aromatic ring\\
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II-1-7 & i5 & charge group\\
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II-1-8 & i5 & polarization group\\
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II-1-9 & f12.6 & atomic partial charge\\
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II-1-10 & f12.6 & atomic polarizability\\
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\hline
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\mc{3}{l}{Any number of cards in deck III to specify complete
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connectivity} \\
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\hline
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III-1-1 & 16i5 & connectivity, duplication allowed\\
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\hline\hline
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\end{tabular}
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\caption{The format of fragment files.\label{tbl:nwafrag}}
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\end{center}
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\end{table}
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\section{Creating segment files}
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\label{sec:nwanwsgm}
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The \prepare\ module is used to generate segment files
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from corresponding fragment files. A segment file contains all
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information for the calculation of bonded and non-bonded interactions
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for a given chemical system using a specific force field.
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Which atoms form a fragment is specified in the coordinate file,
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currently only in PDB format.
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the restriction is that bonded interactions may only involve atoms on at
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most two segments does no longer exist as of \nwchem\ release 3.2.1.
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The segment entries define three sets of parameters
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for each interaction.
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Free energy perturbations can be performed using set 1 for the
|
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generation of the ensemble while using sets 2 and/or 3
|
|
as perturbations. Free energy multiconfiguration thermodynamic
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|
integration and multistep thermodynamic perturbation calculations are
|
|
performed by gradually changing the interactions in the system from
|
|
parameter set 2 to parameter set 3. These modifications can be
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edited into the segment files manually, or introduced directly into
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the topology file using the \verb+modify+ commands in the input for
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the \prepare\ module.
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The format of a segment is
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described in Tables \ref{tbl:nwaseg1}--\ref{tbl:nwaseg6}.
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\begin{table}[htbp]
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\begin{center}
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\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
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\hline\hline
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Deck & Format & Description \\ \hline
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I-0-1 & & \# lines at top are comments \\
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I-1-1 & a1 & \$ to identify the start of a segment \\ %$ for emacs
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I-1-2 & a10 & name of the segment, the tenth character\\
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& & N: identifies beginning of a chain\\
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& & C: identifies end of a chain\\
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& & blank: identifies chain fragment\\
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& & M: identifies an integral molecule\\
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I-2-1 & i5 & number of atoms in the segment\\
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I-2-2 & i5 & number of bonds in the segment\\
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I-2-3 & i5 & number of angles in the segment\\
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I-2-4 & i5 & number of proper dihedrals in the segment\\
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I-2-5 & i5 & number of improper dihedrals in the segment\\
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\hline
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\end{tabular*}
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\caption{Segment file format, table 1 of 6.\label{tbl:nwaseg1}}
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\end{center}
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\end{table}
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|
|
\begin{table}[htbp]
|
|
\begin{center}
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|
\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
|
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\hline\hline
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Deck & Format & Description \\ \hline
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\mc{3}{l}{For each atom one deck II} \\
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II-1-1 & i5 & atom sequence number \\
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II-1-2 & a6 & atom name \\
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|
II-1-3 & a5 & atom type, generic set 1 \\
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II-1-4 & a1 & dynamics type\\
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& & \verb+ + : normal\\
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& & \verb+D+ : dummy atom\\
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& & \verb+S+ : solute interactions only\\
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& & \verb+Q+ : quantum atom\\
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& & other : intramolecular solute interactions only\\
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II-1-4 & a5 & atom type, generic set 2 \\
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II-1-5 & a1 & dynamics type\\
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& & \verb+ + : normal\\
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& & \verb+D+ : dummy atom\\
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|
& & \verb+S+ : solute interactions only\\
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|
& & \verb+Q+ : quantum atom\\
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& & other : intramolecular solute interactions only\\
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|
II-1-6 & a5 & atom type, generic set 3 \\
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II-1-7 & a1 & dynamics type\\
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& & \verb+ + : normal\\
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& & \verb+D+ : dummy atom\\
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& & \verb+S+ : solute interactions only\\
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& & \verb+Q+ : quantum atom\\
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& & other : intramolecular solute interactions only\\
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II-1-8 & i5 & charge group\\
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II-1-9 & i5 & polarization group\\
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II-1-10 & i5 & link number\\
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II-1-11 & i5 & environment type\\
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& & 0: no special identifier\\
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& & 1: planar, using improper torsion\\
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& & 2: tetrahedral, using improper torsion\\
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& & 3: tetrahedral, using improper torsion\\
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& & 4: atom in aromatic ring\\
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II-2-1 & f12.6 & atomic partial charge in e, set 1\\
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II-2-2 & f12.6 & atomic polarizability/$4\pi\epsilon_o$ in nm$^3$, set 1\\
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II-2-3 & f12.6 & atomic partial charge in e, set 2\\
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II-2-4 & f12.6 & atomic polarizability/$4\pi\epsilon_o$ in nm$^3$, set 2\\
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|
II-2-5 & f12.6 & atomic partial charge in e, set 3\\
|
|
II-2-6 & f12.6 & atomic polarizability/$4\pi\epsilon_o$ in nm$^3$, set 3\\
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|
\hline
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\end{tabular*}
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|
\caption{Segment file format, table 2 of 6.\label{tbl:nwaseg2}}
|
|
\end{center}
|
|
\end{table}
|
|
|
|
\begin{table}[htbp]
|
|
\begin{center}
|
|
\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
|
|
\hline\hline
|
|
Deck & Format & Description \\ \hline
|
|
\mc{3}{l}{For each bond a deck III} \\
|
|
III-1-1 & i5 & bond sequence number \\
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|
III-1-2 & i5 & bond atom i \\
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|
III-1-3 & i5 & bond atom j \\
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|
III-1-4 & i5 & bond type \\
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& & 0: harmonic\\
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& & 1: constrained bond\\
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|
III-1-5 & i5 & bond parameter origin\\
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& & 0: from database, next card ignored \\
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& & 1: from next card\\
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|
III-2-1 & f12.6 & bond length in nm, set 1\\
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III-2-2 & e12.5 & bond force constant in kJ nm$^2$ mol$^{-1}$, set 1 \\
|
|
III-2-3 & f12.6 & bond length in nm, set 2\\
|
|
III-2-4 & e12.5 & bond force constant in kJ nm$^2$ mol$^{-1}$, set 2 \\
|
|
III-2-5 & f12.6 & bond length in nm, set 3\\
|
|
III-2-6 & e12.5 & bond force constant in kJ nm$^2$ mol$^{-1}$, set 3 \\
|
|
\hline
|
|
\end{tabular*}
|
|
\caption{Segment file format, table 3 of 6.\label{tbl:nwaseg3}}
|
|
\end{center}
|
|
\end{table}
|
|
|
|
\begin{table}
|
|
\begin{center}
|
|
\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
|
|
\hline\hline
|
|
Deck & Format & Description \\ \hline
|
|
\mc{3}{l}{For each angle a deck IV} \\
|
|
IV-1-1 & i5 & angle sequence number \\
|
|
IV-1-2 & i5 & angle atom i \\
|
|
IV-1-3 & i5 & angle atom j \\
|
|
IV-1-4 & i5 & angle atom k \\
|
|
IV-1-5 & i5 & angle type \\
|
|
& & 0: harmonic\\
|
|
IV-1-6 & i5 & angle parameter origin\\
|
|
& & 0: from database, next card ignored \\
|
|
& & 1: from next card\\
|
|
IV-2-1 & f12.6 & angle in radians, set 1\\
|
|
IV-2-2 & e12.5 & angle force constant in kJ mol$^{-1}$, set 1 \\
|
|
IV-2-3 & f12.6 & angle in radians, set 2\\
|
|
IV-2-4 & e12.5 & angle force constant in kJ mol$^{-1}$, set 2 \\
|
|
IV-2-5 & f12.6 & angle in radians, set 3\\
|
|
IV-2-6 & e12.5 & angle force constant in kJ mol$^{-1}$, set 3 \\
|
|
\hline
|
|
\end{tabular*}
|
|
\caption{Segment file format, table 4 of 6.\label{tbl:nwaseg4}}
|
|
\end{center}
|
|
\end{table}
|
|
|
|
\begin{table}[htbp]
|
|
\begin{center}
|
|
\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
|
|
\hline\hline
|
|
Deck & Format & Description \\ \hline
|
|
\mc{3}{l}{For each proper dihedral a deck V} \\
|
|
V-1-1 & i5 & proper dihedral sequence number \\
|
|
V-1-2 & i5 & proper dihedral atom i \\
|
|
V-1-3 & i5 & proper dihedral atom j \\
|
|
V-1-4 & i5 & proper dihedral atom k \\
|
|
V-1-5 & i5 & proper dihedral atom l \\
|
|
V-1-6 & i5 & proper dihedral type \\
|
|
& & 0: $C\cos(m\phi-\delta)$\\
|
|
V-1-7 & i5 & proper dihedral parameter origin\\
|
|
& & 0: from database, next card ignored \\
|
|
& & 1: from next card\\
|
|
V-2-1 & i5 & multiplicity, set 1\\
|
|
V-2-2 & f12.6 & proper dihedral in radians, set 1\\
|
|
V-2-3 & e12.5 & proper dihedral force constant in kJ mol$^{-1}$, set 1 \\
|
|
V-2-4 & i5 & multiplicity, set 2\\
|
|
V-2-5 & f12.6 & proper dihedral in radians, set 2\\
|
|
V-2-6 & e12.5 & proper dihedral force constant in kJ mol$^{-1}$, set 2 \\
|
|
V-2-7 & i5 & multiplicity, set 3\\
|
|
V-2-8 & f12.6 & proper dihedral in radians, set 3\\
|
|
V-2-9 & e12.5 & proper dihedral force constant in kJ mol$^{-1}$, set 3 \\
|
|
\hline
|
|
\end{tabular*}
|
|
\caption{Segment file format, table 5 of 6.\label{tbl:nwaseg5}}
|
|
\end{center}
|
|
\end{table}
|
|
|
|
\begin{table}[htbp]
|
|
\begin{center}
|
|
\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
|
|
\hline\hline
|
|
Deck & Format & Description \\ \hline
|
|
\mc{3}{l}{For each improper dihedral a deck VI} \\
|
|
VI-1-1 & i5 & improper dihedral sequence number \\
|
|
VI-1-2 & i5 & improper dihedral atom i \\
|
|
VI-1-3 & i5 & improper dihedral atom j \\
|
|
VI-1-4 & i5 & improper dihedral atom k \\
|
|
VI-1-5 & i5 & improper dihedral atom l \\
|
|
VI-1-6 & i5 & improper dihedral type \\
|
|
& & 0: harmonic\\
|
|
VI-1-7 & i5 & improper dihedral parameter origin\\
|
|
& & 0: from database, next card ignored \\
|
|
& & 1: from next card\\
|
|
VI-2-1 & f12.6 & improper dihedral in radians, set 1\\
|
|
VI-2-2 & e12.5 & improper dihedral force constant in kJ mol$^{-1}$, set 1 \\
|
|
VI-2-3 & f12.6 & improper dihedral in radians, set 2\\
|
|
VI-2-4 & e12.5 & improper dihedral force constant in kJ mol$^{-1}$, set 2 \\
|
|
VI-2-5 & f12.6 & improper dihedral in radians, set 3\\
|
|
VI-2-6 & e12.5 & improper dihedral force constant in kJ mol$^{-1}$, set 3 \\
|
|
\hline\hline
|
|
\end{tabular*}
|
|
\caption{Segment file format, table 6 of 6.\label{tbl:nwaseg6}}
|
|
\end{center}
|
|
\end{table}
|
|
|
|
|
|
\section{Creating sequence files}
|
|
A sequence file describes a molecular system in terms of segments. This
|
|
file is generated by the \prepare\ module for the molecular system
|
|
provided on a PDB-formatted coordinate file.
|
|
The file format is given in Table \ref{tbl:nwaseq}
|
|
|
|
\begin{table}[htbp]
|
|
\begin{center}
|
|
\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
|
|
\hline\hline
|
|
Card & Format & Description \\ \hline
|
|
I-1-1 & a1 & \$ to identify the start of a sequence \\ %$ for emacs
|
|
I-1-2 & a10 & name of the sequence\\
|
|
\mc{3}{l}{Any number of cards 1 and 2 in deck II to specify the system} \\
|
|
II-1-1 & i5 & segment number\\
|
|
II-1-2 & a10 & segment name, last character will be determined from chain\\
|
|
II-1-3 & i5 & link segment 1, if blank previous segment in chain\\
|
|
II-1-4 & i3 & link atom, if blank link atom 2\\
|
|
II-1-5 & i5 & link segment 2, if blank next segment in chain\\
|
|
II-1-6 & i3 & link atom, if blank link atom 1\\
|
|
II-1-7 & i5 & link segment 3\\
|
|
II-1-8 & i3 & link atom in link segment 3\\
|
|
II-1-9 & i5 & link segment 4\\
|
|
II-1-0 & i3 & link atom in link segment 4\\
|
|
II-1-1 & i5 & link segment 5\\
|
|
II-1-2 & i3 & link atom in link segment 5\\
|
|
II-1-3 & i5 & link segment 6\\
|
|
II-1-4 & i3 & link atom in link segment 6\\
|
|
II-1-5 & i5 & link segment 7\\
|
|
II-1-6 & i3 & link atom in link segment 7\\
|
|
II-1-7 & i5 & link segment 8\\
|
|
II-1-8 & i3 & link atom in link segment 8\\
|
|
II-1-9 & i5 & link segment 9\\
|
|
II-1-0 & i3 & link atom in link segment 9\\
|
|
II-1-1 & i5 & link segment 10\\
|
|
II-1-2 & i3 & link atom in link segment 10\\
|
|
II-2-1 & a & \verb+break+ to identify a break in the molecule chain\\
|
|
II-2-1 & a & \verb+molecule+ to identify the end of a solute molecule\\
|
|
II-2-1 & a & \verb+fraction+ to identify the end of a solute fraction\\
|
|
II-2-1 & a5 & \verb+link + to specify a link\\
|
|
II-2-2 & i5 & segment number of first link atom\\
|
|
II-2-3 & a4 & name of first link atom \\
|
|
II-2-4 & i5 & segment number of second link atom\\
|
|
II-2-5 & a4 & name of second link atom \\
|
|
II-2-1 & a & \verb+solvent+ to identify solvent definition on next card\\
|
|
II-2-1 & a & \verb+stop+ to identify the end of the sequence\\
|
|
II-2-1 & a6 & \verb+repeat+ to repeat next $ncard$ cards $ncount$
|
|
times\\
|
|
II-2-2 & i5 & number of cards to repeat ($ncards$)\\
|
|
II-2-3 & i5 & number of times to repeat cards ($ncount$)\\
|
|
\mc{3}{l}{Any number of cards in deck II to specify the system} \\
|
|
\hline\hline
|
|
\end{tabular*}
|
|
\caption{Sequence file format.\label{tbl:nwaseq}}
|
|
\end{center}
|
|
\end{table}
|
|
|
|
\section{Creating topology files}
|
|
\label{sec:nwanwtop}
|
|
|
|
The topology (Section \ref{sec:nwatopology}) describes all static information
|
|
that describes a molecular system. This includes the connectivity in
|
|
terms of bond-stretching, angle-bending and torsional interactions, as well as
|
|
the non-bonded van der Waals and Coulombic interactions.
|
|
|
|
The topology of a molecular system is generated by the \prepare\ module
|
|
from the sequence in terms of segments as specified on the PDB file.
|
|
For each unique segment specified in this file the
|
|
segment database directories are searched for the segment definition.
|
|
For segments not found in one of the database directories a segment definition
|
|
is generated in the temporary directory if a fragment file was found.
|
|
If a fragment file could not be found, it is generated by the \prepare\ module
|
|
base on what is found on the PDB file.
|
|
|
|
When all segments are found or created, the parameter substitutions are
|
|
performed, using force field parameters taken from the parameter
|
|
databases. After all lists have been generated the
|
|
topology is written to a local topology file \verb+$system$.top+.
|
|
|
|
\section{Creating restart files}
|
|
\label{sec:nwanwrst}
|
|
|
|
Restart files contain all dynamical information about a molecular
|
|
system and are created by the \prepare\ module if a topology file
|
|
is available. The \prepare\ module will automatically generate
|
|
coordinates for hydrogen atoms and monatomic counter ions
|
|
not found on the PDB formatted coordinate file, if no fragment or
|
|
segment files were generated using that PDB file.
|
|
|
|
The \prepare\ module has a number of other optional input command,
|
|
including solvation.
|
|
|
|
\section{Molecular simulations}
|
|
The type of molecular dynamics simulation is specified by the
|
|
\nwchem\ task directive.
|
|
\begin{verbatim}
|
|
task md [ energy || optimize || dynamics || thermodynamics ]
|
|
\end{verbatim}
|
|
where the theory keyword {\tt md} specifies use of the molecular
|
|
dynamics module, and the operation keyword is one of
|
|
\begin{description}
|
|
\item
|
|
{\tt energy} for single configuration energy evaluation
|
|
\item
|
|
{\tt optimize} for energy minimization
|
|
\item
|
|
{\tt dynamics} for molecular dynamics simulations and single step
|
|
thermodynamic perturbation free energy molecular dynamics simulations
|
|
\item
|
|
{\tt thermodynamics} for combined multi-configuration thermodynamic
|
|
integration and multiple step thermodynamic perturbation free
|
|
energy molecular dynamics simulations.
|
|
\end{description}
|
|
|
|
\section{System specification}
|
|
The chemical system for a calculation is specified in the topology
|
|
and restart files. These files should be created using the utilities
|
|
\nwtop\ and \nwrst\ before a simulation can be performed.
|
|
The names of these files are determined from the \nwchem\ \verb+start+
|
|
directive.
|
|
There is no default. If the \verb+rtdb+ name is given as {\tt system\_calc},
|
|
the topology file used is {\tt system.top}, while all other files
|
|
are named {\tt system\_calc.ext}.
|
|
|
|
\section{Parameter set}
|
|
\begin{description}
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
set <integer iset>
|
|
\end{verbatim}
|
|
specifies the use of parameter set \verb+<iset>+ for the
|
|
molecular dynamics simulation.
|
|
The topology file contains three separate parameters sets that can
|
|
be used. The default for \verb+<iset>+ is 1.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
pset <integer isetp1> [<integer isetp2>]
|
|
\end{verbatim}
|
|
specifies the parameter sets to be used as perturbation potentials
|
|
in single step thermodynamic perturbation free energy evaluations,
|
|
where \verb+<isetp1>+ specifies the first perturbation parameter set and
|
|
\verb+<isetp2>+ specifies the second perturbation parameter set. Legal
|
|
values for \verb+<isetp1>+ are 2 and 3. Legal value for \verb+<isetp2>+ is
|
|
3, in which case \verb+<isetp1>+ can only be 2. If specified, \verb+<iset>+
|
|
is automatically set to 1.
|
|
\end{description}
|
|
|
|
\section{Energy minimization algorithms}
|
|
The energy minimization of the system as found in the restart file
|
|
is performed with the following directives. If both are specified,
|
|
steepest descent energy minimization precedes conjugate gradient
|
|
minimization.
|
|
|
|
%\begin{description}
|
|
\begin{description}
|
|
\item
|
|
\begin{verbatim}
|
|
sd <integer msdit> [init <real dx0sd>] [min <real dxsdmx>] \
|
|
[max <real dxmsd>]
|
|
\end{verbatim}
|
|
specifies the variables for steepest descent energy minimizations,
|
|
where \verb+<msdit>+ is the maximum number of steepest descent steps taken,
|
|
for which the default is 100, \verb+<dx0sd>+ is the initial step size in nm
|
|
for which the default is 0.001, \verb+<dxsdmx>+ is the threshold for the
|
|
step size in nm for which the default is 0.0001, and \verb+<dxmsd>+ is the
|
|
maximum allowed step size in nm for which the default is 0.05.
|
|
\item
|
|
\begin{verbatim}
|
|
cg <integer mcgit> [init <real dx0cg>] [min <real dxcgmx>] \
|
|
[cy <integer ncgcy>]
|
|
\end{verbatim}
|
|
specifies the variables for conjugate gradient energy minimizations,
|
|
where \verb+<mcgit>+ is the maximum number of conjugate gradient steps
|
|
taken, for which the default is 100, \verb+<dx0cg>+ is the initial search
|
|
interval size in nm for which the default is 0.001, \verb+<dxcgmx>+ is the
|
|
threshold for the step size in nm for which the default is 0.0001, and
|
|
\verb+<ncgcy>+ is the number of conjugate gradient steps after which the
|
|
gradient history is discarded for which the default is 10. If conjugate
|
|
gradient energy minimization is preceded by steepest descent energy
|
|
minimization, the search interval is set to twice the final step of the
|
|
steepest descent energy minimization.
|
|
\end{description}
|
|
%\end{description}
|
|
|
|
\section{Multi-configuration thermodynamic integration}
|
|
The following keywords control free energy difference simulations.
|
|
Multi-configuration thermodynamic integrations are always combined
|
|
with multiple step thermodynamic perturbations.
|
|
\begin{description}
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
(forward || reverse) [[<integer mrun> of] <integer maxlam>]
|
|
\end{verbatim}
|
|
specifies the direction and number of integration steps in free
|
|
energy evaluations, with {\tt forward} being the default direction.
|
|
\verb+<mrun>+ is the number of ensembles that will be generated in
|
|
this calculation, and \verb+<maxlam>+ is the total number of ensembles
|
|
to complete the thermodynamic integration. The default value for
|
|
\verb+<maxlam>+ is 21. The default value of \verb+<mrun>+ is the
|
|
value of \verb+<maxlam>+.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
error <real edacq>
|
|
\end{verbatim}
|
|
specifies the maximum allowed statistical error in each generated
|
|
ensemble, where \verb+<edacq>+ is the maximum error allowed in the
|
|
ensemble average derivative of the Hamiltonian with respect to
|
|
$\lambda$ with a default of 5.0 kJ~mol$^{-1}$.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
drift <real ddacq>
|
|
\end{verbatim}
|
|
specifies the maximum allowed drift in the free energy result,
|
|
where \verb+<ddacq>+ is the maximum drift allowed in the
|
|
ensemble average derivative of the Hamiltonian with respect to
|
|
$\lambda$with a default of 5.0 kJ~mol$^{-1}$ps$^{-1}$.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
factor <real fdacq>
|
|
\end{verbatim}
|
|
specifies the maximum allowed change in ensemble size
|
|
where \verb+<fdacq>+ is the minimum size of an ensemble relative to the
|
|
previous ensemble in the calculation with a default value of 0.75.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
decomp
|
|
\end{verbatim}
|
|
specifies that a free energy decomposition is to be carried out.
|
|
Since free energy contributions are path dependent, results from a
|
|
decomposition analysis can not be unambiguously interpreted, and
|
|
the default is not to perform this decomposition.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
sss [delta <real delta>]
|
|
\end{verbatim}
|
|
specifies that atomic non-bonded interactions describe a dummy atom
|
|
in either the initial or final state of the thermodynamic calculation
|
|
will be calculated using separation-shifted scaling, where \verb+<delta>+
|
|
is the separation-shifted scaling factor with a default of 0.075 nm$^2$.
|
|
This scaling method prevents problems associated with singularities in
|
|
the interaction potentials.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
new || renew || extend
|
|
\end{verbatim}
|
|
specifies the initial conditions for thermodynamic calculations.
|
|
{\tt new} indicates that this is an initial mcti calculation, which
|
|
is the default. {\tt renew} instructs to obtain the initial
|
|
conditions for each $\lambda$ from the {\bf mro}-file from a previous
|
|
mcti calculation, which has to be renamed to an {\bf mri}-file. The
|
|
keyword {\tt extend} will extend a previous mcti calculation from the
|
|
data read from an {\bf mri}-file.
|
|
\end{description}
|
|
|
|
\section{Time and integration algorithm directives}
|
|
Following directives control the integration of the equations of motion.
|
|
\begin{description}
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
leapfrog || vverlet
|
|
\end{verbatim}
|
|
specifies the integration algorithm,
|
|
where {\tt leapfrog} specifies the default leap frog integration, and
|
|
{\tt vverlet} specifies the velocity Verlet integrator.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
equil <integer mequi>
|
|
\end{verbatim}
|
|
specifies the number of equilibration steps \verb+<mequi>+, with a default
|
|
of 100.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
data <integer mdacq> [over <integer ldacq>]]
|
|
\end{verbatim}
|
|
specifies the number of data gathering steps \verb+<mdacq>+ with a
|
|
default of 500. In multi-configuration thermodynamic integrations
|
|
\verb+<mequi>+ and \verb+<mdacq>+ are for each of the ensembles, and
|
|
variable \verb+<ldacq>+ specifies the minimum number of data gathering steps
|
|
in each ensemble. In regular molecular dynamics simulations \verb+<ldacq>+
|
|
is not used. The default value for \verb+<ldacq>+ is the value of \verb+<mdacq>+.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
time <real stime>
|
|
\end{verbatim}
|
|
specifies the initial time \verb+<stime>+ of a molecular simulation in ps,
|
|
with a default of 0.0.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
step <real tstep>
|
|
\end{verbatim}
|
|
specifies the time step \verb+<tstep>+ in ps, with 0.001 as the default value.
|
|
\end{description}
|
|
|
|
\section{Ensemble selection}
|
|
Following directives control the ensemble type.
|
|
|
|
\begin{description}
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
isotherm [<real tmpext>] [trelax <real tmprlx> [<real tmsrlx>]]
|
|
\end{verbatim}
|
|
specifies a constant temperature ensemble using Berendsen's thermostat,
|
|
where \verb+<tmpext>+ is the external temperature with a default of 298.15~K,
|
|
and \verb+<tmprlx>+ and \verb+<tmsrlx>+ are temperature relaxation times in ps
|
|
with a default of 0.1. If only \verb+<tmprlx>+ is given the complete system
|
|
is coupled to the heat bath with relaxation time \verb+<tmprlx>+. If both
|
|
relaxation times are supplied, solvent and solute are independently coupled
|
|
to the heat bath with relaxation times \verb+<tmprlx>+ and \verb+<tmsrlx>+,
|
|
respectively.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
isobar [<real prsext>] [trelax <real prsrlx> ] \
|
|
[compress <real compr>]
|
|
\end{verbatim}
|
|
specifies a constant pressure ensemble using Berendsen's piston,
|
|
where \verb+<prsext>+ is the external pressure with a default of 1.025~10$^5$ Pa,
|
|
\verb+<prsrlx>+ is the pressure relaxation time in ps with a default of 0.5, and
|
|
\verb+<compr>+ is the system compressibility in m$^2$N$^{-1}$ with a
|
|
default of 4.53E-10.
|
|
\end{description}
|
|
|
|
\section{Velocity reassignments}
|
|
Velocities can be periodically reassigned to reflect a certain temperature.
|
|
\begin{description}
|
|
\item
|
|
\begin{verbatim}
|
|
vreass <integer nfgaus> <real tgauss>
|
|
\end{verbatim}
|
|
specifies that velocities will be reassigned every \verb+<nfgaus>+ molecular
|
|
dynamics steps, reflecting a temperature of \verb+<tgauss>+~K. The default
|
|
is not to reassign velocities, i.e.\ \verb+<nfgaus>+ is 0.
|
|
\end{description}
|
|
|
|
\section{Cutoff radii}
|
|
Cutoff radii can be specified for short range and long range interactions.
|
|
\begin{description}
|
|
\item
|
|
\begin{verbatim}
|
|
cutoff [short] <real rshort> [long <real rlong>] \
|
|
[qmmm <real rqmmm>]
|
|
\end{verbatim}
|
|
specifies the short range cutoff radius \verb+<rshort>+, and the long range
|
|
cutoff radius \verb+<rlong>+ in nm. If the long range cutoff radius
|
|
is larger than the short range cutoff radius the twin range method will
|
|
be used, in which short range forces and energies are evaluated every
|
|
molecular dynamics step, and long range forces and energies with a
|
|
frequency of \verb+<nflong>+ molecular dynamics steps. Keyword
|
|
\verb+qmmm+ specifies the radius of the zone around quantum atoms
|
|
defining the QM/MM bare charges.
|
|
The default value for \verb+<rshort>+, \verb+<rlong>+ and \verb+<rqmmm>+
|
|
is 0.9~nm.
|
|
\end{description}
|
|
|
|
\section{Polarization}
|
|
First order and self consistent electronic polarization models have
|
|
been implemented.
|
|
\begin{description}
|
|
\item
|
|
\begin{verbatim}
|
|
polar (first || scf [[<integer mpolit>] <real ptol>])
|
|
\end{verbatim}
|
|
specifies the use of polarization potentials,
|
|
where the keyword {\tt first} specifies the first order polarization
|
|
model, and {\tt scf} specifies the self consistent polarization field
|
|
model, iteratively determined with a maximum of \verb+<mpolit>+
|
|
iterations to within a tolerance of \verb+<ptol>+ D in the generated
|
|
induced dipoles. The default is not to use polarization models.
|
|
\end{description}
|
|
|
|
\section{External electrostatic field}
|
|
\begin{description}
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
field <real xfield> [freq <real xffreq>] [vector <real xfvect(1:3)>]
|
|
\end{verbatim}
|
|
specifies an external electrostatic field,
|
|
where \verb+<xfield>+ is the field strength, \verb+<xffreq>+ is the
|
|
frequency in MHz and \verb+<xfvect>+ is the external field vector.
|
|
\end{description}
|
|
|
|
\section{Constraints}
|
|
Constraints are satisfied using the SHAKE
|
|
coordinate resetting procedure.
|
|
\begin{description}
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
shake [<integer mshitw> [<integer mshits>]] \
|
|
[<real tlwsha> [<real tlssha>]]
|
|
\end{verbatim}
|
|
specifies the use of SHAKE constraints,
|
|
where \verb+<mshitw>+ is the maximum number of solvent SHAKE iterations,
|
|
and \verb+<mshits>+ is the maximum number of solute SHAKE iterations. If
|
|
only \verb+<mshitw>+ is specified, the value will also be used for \verb+<mshits>+.
|
|
The default maximum number of iterations is 100 for both.
|
|
\verb+<tlwsha>+ is the solvent SHAKE tolerance in nm, and \verb+<tlssha>+ is
|
|
the solute SHAKE tolerance in nm. If only \verb+<tlwsha>+ is specified, the
|
|
value given will also be used for \verb+<tlssha>+. The default tolerance
|
|
is 0.001~nm for both.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
noshake (solvent || solute)
|
|
\end{verbatim}
|
|
disables SHAKE and treats the bonded interaction according to the force
|
|
field.
|
|
|
|
\end{description}
|
|
|
|
\section{Long range interaction corrections}
|
|
Long range electrostatic interactions are implemented using the
|
|
smooth particle mesh Ewald technique, for neutral periodic cubic systems in
|
|
the constant volume ensemble, using pair interaction potentials. Particle-mesh
|
|
Ewald long range interactions can only be used in molecular dynamics simulations
|
|
using effective pair potentials, and not in free energy simulations, QMD or
|
|
QM/MM simulations.
|
|
|
|
\begin{description}
|
|
\item
|
|
\begin{verbatim}
|
|
pme [grid <integer ng>] [alpha <real ealpha>] \
|
|
[order <integer morder>] [fft <integer imfft>]
|
|
\end{verbatim}
|
|
specifies the use of smooth particle-mesh Ewald long range
|
|
interaction treatment,
|
|
where \verb+ng+ is the number of grid points per dimension,
|
|
\verb+ealpha+ is the Ewald coefficient in nm$^{-1}$, with a default
|
|
that leads to a tolerance of $10^{-4}$ at the short range cutoff radius,
|
|
and \verb+morder+ is order of the Cardinal B-spline
|
|
interpolation which must be an even number and at least 4 (default
|
|
value). A platform specific 3D fast Fourier transform is used, if
|
|
available, when \verb+imfft+ is set to 2.
|
|
\end{description}
|
|
|
|
\section{Fixing coordinates}
|
|
The solvent or solute part of a system may be fixed or unfixed using
|
|
the following keywords. Fixing part of the system will not propagate to
|
|
simulations using restart files written. In the commands \verb+fix+
|
|
and \verb+unfix+, the keywords \verb+all+, \verb+solvent+,
|
|
\verb+solute+ and \verb+non-H+ specify the entire molecular system,
|
|
the solvent, the solute and the solute atoms other than hydrogen,
|
|
respectively.
|
|
\begin{description}
|
|
\item
|
|
\begin{verbatim}
|
|
fix (all || solvent || solute || non-H)
|
|
\end{verbatim}
|
|
fixes all atoms, solvent molecule, solute atom or solute non-hydrogen atoms,
|
|
respectively.
|
|
\item
|
|
\begin{verbatim}
|
|
unfix (all || solvent || solute || non-H)
|
|
\end{verbatim}
|
|
makes all atoms, solvent molecule, solute atom or solute non-hydrogen atoms,
|
|
respectively, dynamic.
|
|
\end{description}
|
|
|
|
\section{Autocorrelation function}
|
|
For the evaluation of the statistical error of multi-configuration
|
|
thermodynamic integration free energy results a correlated data
|
|
analysis is carried out, involving the calculation of the
|
|
autocorrelation function of the derivative of the Hamiltonian with
|
|
respect to the control variable $\lambda$.
|
|
\begin{description}
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
auto <integer lacf> [fit <integer nfit>] [weight <real weight>]
|
|
\end{verbatim}
|
|
controls the calculation of the autocorrelation,
|
|
where \verb+<lacf>+ is the length of the autocorrelation function, with
|
|
a default of 1000, \verb+<nfit>+ is the number of functions used in the
|
|
fit of the autocorrelation function, with a default of 15, and
|
|
\verb+<weight>+ is the weight factor for the autocorrelation function,
|
|
with a default value of 0.0.
|
|
\end{description}
|
|
|
|
\section{Print options}
|
|
Keywords that control print to the output file, with extension {\bf out}.
|
|
Print directives may be combined to a single directive.
|
|
|
|
\begin{description}
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
print topol [nonbond] [solvent] [solute]
|
|
\end{verbatim}
|
|
specifies printing the topology information,
|
|
where {\tt nonbond} refers to the non-bonded interaction parameters,
|
|
{\tt solvent} to the solvent bonded parameters, and {\tt solute} to the
|
|
solute bonded parameters. If only {\tt topol} is specified, all
|
|
topology information will be printed to the output file.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
print step <integer nfoutp> [extra] [energy]
|
|
\end{verbatim}
|
|
specifies the frequency \verb+nfoutp+ of printing molecular dynamics step
|
|
information to the output file. If the keyword {\tt extra} is specified
|
|
additional energetic data are printed for solvent and solute separately.
|
|
If the keyword {\tt energy} is specified, information is printed for
|
|
all bonded solute interactions.
|
|
The default for \verb+nfoutp+ is 0. For molecular dynamics simulations
|
|
this frequency is in time steps, and for multi-configuration thermodynamic
|
|
integration in $\lambda$-steps.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
print stat <integer nfstat>
|
|
\end{verbatim}
|
|
specifies the frequency \verb+<nfstat>+ of printing statistical information
|
|
of properties that are calculated during the simulation.
|
|
For molecular dynamics simulation
|
|
this frequency is in time steps, for multi-configuration thermodynamic
|
|
integration in $\lambda$-steps.
|
|
\end{description}
|
|
|
|
\section{Periodic updates}
|
|
Following keywords control periodic events during a molecular
|
|
dynamics or thermodynamic integration simulation.
|
|
Update directives may be combined to a single directive.
|
|
|
|
\begin{description}
|
|
\item
|
|
\begin{verbatim}
|
|
update pairs <integer nfpair>
|
|
\end{verbatim}
|
|
specifies the frequency \verb+<nfpair>+ in molecular dynamics steps of
|
|
updating the pair lists. The default for the frequency is 1.
|
|
In addition, pair lists are also updated after each step in which
|
|
recording of the restart or trajectory files is performed. Updating
|
|
the pair lists includes the redistribution of atoms that changed
|
|
domain and load balancing, if specified.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
update long <integer nflong>
|
|
\end{verbatim}
|
|
specifies the frequency \verb+<nflong>+ in molecular dynamics steps
|
|
of updating the long range forces. The default frequency is 1.
|
|
The distinction of short range and long range forces is only
|
|
made if the long range cutoff radius was specified to be larger
|
|
than the short range cutoff radius. Updating the long range forces
|
|
is also done in every molecular dynamics step in which the
|
|
pair lists are regenerated.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
update center <integer nfcntr> [fraction <integer idscb(1:5)>]
|
|
\end{verbatim}
|
|
specifies the frequency \verb+<nfcntr>+ in molecular dynamics steps in
|
|
which the center of geometry of the solute(s) is translated to the
|
|
center of the simulation volume. The solute fractions determining the
|
|
solutes that will be centered are specified by the keyword
|
|
{\tt fraction} and the vector \verb+<idscb>+, with a maximum of 5 entries.
|
|
This translation is implemented such that it has no effect on any
|
|
aspect of the simulation. The default is not to center, i.e. nfcntr is
|
|
0. The default fraction used to center solute is 1.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
update motion <integer nfslow>
|
|
\end{verbatim}
|
|
specifies the frequency \verb+<nfslow>+ in molecular dynamics steps of
|
|
removing the center of mass motion.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
update analysis <integer nfanal>
|
|
\end{verbatim}
|
|
specifies the frequency \verb+<nfanal>+ in molecular dynamics steps of
|
|
invoking the analysis module.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
update rdf <integer nfrdf> [range <real rrdf>] [bins <integer ngl>]
|
|
\end{verbatim}
|
|
specifies the frequency \verb+<nfrdf>+ in molecular dynamics steps of
|
|
calculating contributions to the radial distribution functions.
|
|
The default is 0. The range of the radial distribution
|
|
functions is given by \verb+<rrdf>+ in nm, with a default of the short
|
|
range cutoff radius. Note that radial distribution functions are not
|
|
evaluated beyond the short range cutoff radius. The number of
|
|
bins in each radial distribution function is given by \verb+<ngl>+, with
|
|
a default of 1000.
|
|
If radial distribution function are to be
|
|
calculated, a {\bf rdi} files needs to be available in which the
|
|
contributions are specified as follows.
|
|
\begin{center}
|
|
\begin{tabular}{lll}
|
|
\hline\hline
|
|
Card & Format & Description \\ \hline
|
|
I-1 & i & Type, 1=solvent-solvent, 2=solvent-solute,
|
|
3-solute-solute\\
|
|
I-2 & i & Number of the rdf for this contribution\\
|
|
I-3 & i & First atom number \\
|
|
I-4 & i & Second atom number \\
|
|
\hline
|
|
\end{tabular}
|
|
\end{center}
|
|
\end{description}
|
|
|
|
\section{Recording}
|
|
The following keywords control recording data to file.
|
|
Record directives may be combined to a single directive.
|
|
|
|
\begin{description}
|
|
|
|
%\item
|
|
%The file format of selected recording files is specified with
|
|
%\begin{verbatim}
|
|
%record (binary || ascii [ecce || argos])
|
|
%\end{verbatim}
|
|
%with the default of ascii in ecce readable format.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
record rest <integer nfrest> [keep]
|
|
\end{verbatim}
|
|
specifies the frequency \verb+<nfrest>+ in molecular dynamics steps
|
|
of rewriting the restart file, with extension \verb+rst+.
|
|
For multi-configuration
|
|
thermodynamic integration simulations the frequency is in
|
|
steps in $\lambda$. The default is not to record. The restart
|
|
file is used to start or restart simulations. The keyword {\tt keep}
|
|
causes all restart files written to be kept on disk, rather than
|
|
to be overwritten.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
record coord <integer nfcoor>
|
|
\end{verbatim}
|
|
specifies the frequency \verb+<nfcoor>+ in molecular dynamics steps
|
|
of writing information to the coordinate file, with extension \verb+coo+.
|
|
For multi-configuration
|
|
thermodynamic integration simulations the frequency is in
|
|
steps in $\lambda$. The default is not to record.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
record scoor <integer nfscoo>
|
|
\end{verbatim}
|
|
specifies the frequency \verb+<nfscoo>+ in molecular dynamics steps
|
|
of writing information to the solute coordinate file, with extension
|
|
\verb+sco+. For multi-configuration
|
|
thermodynamic integration simulations the frequency is in
|
|
steps in $\lambda$. The default is not to record.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
record veloc <integer nfvelo>
|
|
\end{verbatim}
|
|
specifies the frequency \verb+<nfvelo>+ in molecular dynamics steps
|
|
of writing information to the velocity file, with extension \verb+vel+.
|
|
For multi-configuration
|
|
thermodynamic integration simulations the frequency is in
|
|
steps in $\lambda$. The default is not to record.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
record svelo <integer nfsvel>
|
|
\end{verbatim}
|
|
specifies the frequency \verb+<nfsvel>+ in molecular dynamics steps
|
|
of writing information to the solute velocity file, with extension
|
|
\verb+svl+. For multi-configuration
|
|
thermodynamic integration simulations the frequency is in
|
|
steps in $\lambda$. The default is not to record.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
record prop <integer nfprop>
|
|
\end{verbatim}
|
|
specifies the frequency \verb+<nfprop>+ in molecular dynamics steps
|
|
of writing information to the property file, with extension
|
|
\verb+prp+. For multi-configuration
|
|
thermodynamic integration simulations the frequency is in
|
|
steps in $\lambda$. The default is not to record.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
record mind <integer nfem>
|
|
\end{verbatim}
|
|
specifies the frequency \verb+<nfem>+ in energy minimization steps of
|
|
writing the minimization trajectory to file, with extension \verb+emt+.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
record free <integer nffree>
|
|
\end{verbatim}
|
|
specifies the frequency \verb+<nffree>+ in multi-configuration
|
|
thermodynamic integration steps to record data to the
|
|
free energy data file, with extension \verb+gib+.
|
|
The default is 1, i.e.\ to record at every $\lambda$.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
record cnv
|
|
\end{verbatim}
|
|
specifies that free energy convergence data will be written to the
|
|
free energy convergence file, with extension \verb+cnv+.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
record acf
|
|
\end{verbatim}
|
|
specifies that free energy derivative autocorrelation data will be
|
|
written to the free energy autocorrelation file, with extension
|
|
\verb+acf+.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
record fet
|
|
\end{verbatim}
|
|
that free energy vs.\ time data will be recorded to the free energy
|
|
data file, with extension \verb+fet+.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
record sync <integer nfsync>
|
|
\end{verbatim}
|
|
specifies the frequency \verb+<nfsync>+ in molecular dynamics steps
|
|
of writing information to the synchronization file, with extension
|
|
\verb+syn+.
|
|
The default is not to record.
|
|
The information written is the simulation time, the wall clock time
|
|
of the previous MD step, the wall clock time of the previous force
|
|
evaluation, the total synchronization time, the largest
|
|
synchronization time and the node on which the largest synchronization
|
|
time was found. The recording of synchronization times is part of the
|
|
load balancing algorithm. Since load balancing is only performed when
|
|
pair-lists are updated, the frequency \verb+<nfsync>+ is correlated
|
|
with the frequency of pair-list updates \verb+<nfpair>+.
|
|
\end{description}
|
|
|
|
\section{Program control options}
|
|
\begin{description}
|
|
\item
|
|
\begin{verbatim}
|
|
load [reset] ( none || size [<real factld>] || pairs ||
|
|
(pairs [<integer ldpair>] size [<real factld>]) )
|
|
\end{verbatim}
|
|
determines the type of dynamic load balancing performed,
|
|
where the default is {\tt none}. Load balancing option {\tt size}
|
|
is resizing boxes on a node, and {\tt pairs} redistributes the
|
|
box-box interactions over nodes. Keyword \verb+reset+ will reset the
|
|
load balancing read from the restart file. The level of box resizing
|
|
can be influenced with $factld$. The boxes on the busiest node are
|
|
resized with a factor
|
|
\begin{equation}
|
|
\left( 1 - factld * { {T_{sync} \over n_p} - t^{min}_{sync} \over t_{wall}}
|
|
\right)^{1\over 3}
|
|
\end{equation}
|
|
where $T_{sync}$ is the accumulated synchronization time of all nodes,
|
|
$n_p$ is the total number of nodes, $t^{min}_{sync}$ is the synchronization
|
|
time of the busiest node, and $t_{wall}$ is the wall clock time of the
|
|
molecular dynamics step.\\
|
|
For the combined load balancing, \verb+ldpair+ is the number of successive pair
|
|
redistribution load balancing steps in which the accumulated synchronization
|
|
time increases, before a resizing load balancing step will be attempted.\\
|
|
Load balancing is only performed in molecular dynamics steps in which the
|
|
pair-list is updated.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
nodes <integer npx> <integer npy> <integer npz>
|
|
\end{verbatim}
|
|
specifies the distribution of the available nodes over the three
|
|
Cartesian dimensions. The default distribution is chosen such that,
|
|
\verb+<npx>+$*$\verb+<npy>+$*$\verb+<npz>+=\verb+<np>+
|
|
and \verb+<npx>+ $<=$ \verb+<npy>+ $<=$ \verb+<npz>+,
|
|
where \verb+<npx>+, \verb+<npy>+ and \verb+<npz>+ are the nodes in the
|
|
x, y and z dimension respectively, and \verb+<np>+ is the number of nodes
|
|
allocated for the calculation. Where more than one combination
|
|
of \verb+<npx>+, \verb+<npy>+ and \verb+<npz>+ are possible, the
|
|
combination is chosen with the minimum value of
|
|
\verb+<npx>+$+$\verb+<npy>+$+$\verb+<npz>+. To change the default setting
|
|
the following optional input option is provided.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
boxes <integer nbx> <integer nby> <integer nbz>
|
|
\end{verbatim}
|
|
specifies the distribution of boxes,
|
|
where \verb+<nbx>+, \verb+<nby>+ and \verb+<nbz>+ are the number of
|
|
boxes in x, y and z direction, respectively.
|
|
The molecular system is decomposed into boxes that form the smallest
|
|
unit for communication of atomic data between nodes. The size of the
|
|
boxes is per default set to the short-range cutoff radius. If
|
|
long-range cutoff radii are used the box size is set to half the
|
|
long-range cutoff radius if it is larger than the short-range cutoff.
|
|
If the number of boxes in a dimension is less than the number of
|
|
processors in that dimension, the number of boxes is set to the number
|
|
of processors.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
extra <integer madbox>
|
|
\end{verbatim}
|
|
sets the number of additional boxes for which memory is allocated.
|
|
In rare events the amount of memory set aside per node is insufficient
|
|
to hold all atomic coordinates assigned to that node. This leads to
|
|
execution which aborts with the message that {\tt mwm} or {\tt msa} is too
|
|
small. Jobs may be restarted with additional space allocated by
|
|
where \verb+<madbox>+ is the number of additional boxes that are allocated
|
|
on each node. The default for \verb+<madbox>+ is 6.
|
|
In some cases \verb+<madbox>+ can be reduced to 4 if memory usage is a
|
|
concern. Values of 2 or less will almost certainly result in memory
|
|
shortage.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
mwm <integer mwmreq>
|
|
\end{verbatim}
|
|
sets the maximum number of solvent molecules \verb+<mwmreq>+ per node,
|
|
allowing increased memory to be allocated for solvent molecules. This
|
|
option can be used if execution aborted because \verb+mwm+ was too
|
|
small.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
msa <integer msareq>
|
|
\end{verbatim}
|
|
sets the maximum number of solute atoms \verb+<msareq>+ per node,
|
|
allowing increased memory to be allocated for solute atoms. This
|
|
option can be used if execution aborted because \verb+msa+ was too
|
|
small.
|
|
|
|
\item
|
|
\begin{verbatim}
|
|
memory <integer memlim>
|
|
\end{verbatim}
|
|
sets a limit \verb+<memlim>+ in kB on the allocated amount of memory used by
|
|
the molecular dynamics module.
|
|
Per default all available memory is allocated. Use of this command
|
|
is required for QM/MM simulations only.
|
|
%\item
|
|
%For development purposes debug information can be written to the debug
|
|
%file with extension {\bf dbg} with
|
|
%\begin{verbatim}
|
|
%debug <i idebug>
|
|
%\end{verbatim}
|
|
%where $idebug$ specifies the type of debug information being written.
|
|
\end{description}
|