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560 lines
No EOL
16 KiB
TeX
560 lines
No EOL
16 KiB
TeX
%
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% $Id$
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%
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\label{sec:analysis}
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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\nwtop{{\bf nwtop}}
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\def\nwrst{{\bf nwrst}}
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\def\nwsgm{{\bf nwsgm}}
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\def\esp{{\bf esp}}
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\def\md{{\bf md}}
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\def\prepare{{\bf prepare}}
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\def\analysis{{\bf analysis}}
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\def\argos{{\bf ARGOS}}
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\def\amber{{\bf AMBER}}
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\def\charmm{{\bf CHARMM}}
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\def\discover{{\bf DISCOVER}}
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\def\povray{{\bf povray}}
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\def\gopenmol{{\bf gOpenMol}}
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\def\ecce{{\bf ecce}}
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The \analysis\ module is used to analyze molecular trajectories generated
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by the \nwchem\ molecular dynamics module, or partial charges generated
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by the \nwchem\ electrostatic potential fit module. This module should
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not de run in parallel mode.
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Directives for the \analysis\ module are read from an input deck,
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\begin{verbatim}
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analysis
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...
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end
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\end{verbatim}
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The analysis is performed as post-analysis of trajectory files through
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using the {\rm task} directive
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\begin{verbatim}
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task analysis
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\end{verbatim}
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or
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\begin{verbatim}
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task analyze
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\end{verbatim}
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\section{System specification}
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\begin{verbatim}
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system <string systemid>_<string calcid>
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\end{verbatim}
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where the strings \verb+systemid+ and \verb+calcid+ are user defined names
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for the chemical system and the type of calculation to ber performed,
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respectively. These names are used to derive the filenames used for the
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calculation. The topoly file used will be \verb+systemid.top+, while all
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other files are named \verb+systemid_calcid.ext+.
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\section{Reference coordinates}
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Most analyses require a set of reference coordinates. These
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coordinates are read from a \nwchem\ restart file by the directive,
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\begin{verbatim}
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reference <string filename>
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\end{verbatim}
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where {\rm filename} is the name of an existing restart file.
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This input directive is required.
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\section{File specification}
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The trajectory file(s) to be analyzed are specified with
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\begin{verbatim}
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file <string filename> [<integer firstfile> <integer lastfile>]
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\end{verbatim}
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where {\rm filename} is an existing {\rm trj} trajectory file.
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If {\rm firstfile} and {\rm lastfile} are specified, the specified
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{\rm filename} needs to have a {\rm ?} wild card character that will
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be substituted by the 3-character integer number from {\rm firstfile}
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to {\rm lastfile}, and the analysis will be performed on the series
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of files.
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For example,
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\begin{verbatim}
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file tr_md?.trj 3 6
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\end{verbatim}
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will instruct the analysis to be performed on files {\it tr\_md003.trj},
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{\it tr\_md004.trj}, {\it tr\_md005.trj} and {\it tr\_md006.trj}.
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\par
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From the specified files the subset of frames to be analyzed is
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specified by
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\begin{verbatim}
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frames [<integer firstframe default 1>] <integer lastframe> \
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[<integer frequency default 1>]
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\end{verbatim}
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For example, to analyze the first 100 frames from the specified
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trajectory files, use
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\begin{verbatim}
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frames 100
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\end{verbatim}
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To analyze every 10-th frame between frames 200 and 400 recorded on
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the specified trajectory files, use
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\begin{verbatim}
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frames 200 400 10
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\end{verbatim}
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A time offset can be specified with
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\begin{verbatim}
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time <real timoff>
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\end{verbatim}
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Solute coordinates of the reference set and ech subsequent frame
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read from a trajectory file are translated to have the center of
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geometry of the specified solute molecule at the center of the
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simulation box. After this translation all molecules are folded
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back into the box according to the periodic boundary conditions.
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The directive for this operation is
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\begin{verbatim}
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center <integer imol> [<integer jmol default imol>]
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\end{verbatim}
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Coordinates of each frame read from a trajectory file can be
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rotated using
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\begin{verbatim}
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rotate ( off | x | y | z ) <real angle units degrees>
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\end{verbatim}
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If \verb+center+ was defined, rotation takes place after
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the system has been centered. The \verb+rotate+ directives
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only apply to frames read from the trajectory files, and not
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to the reference coordinates. Upto 100 \verb+rotate+ directives
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can be specified, which will be carried out in the order in which
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they appear in the input deck. \verb+rotate off+ cancels all
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previously defined \verb+rotate+ directives.
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To perform a hydrogen bond analysis:
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\begin{verbatim}
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hbond [distance [[<real rhbmin default 0.0>] <real rhbmin>]] \
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[angle [<real hbdmin> [ <real hbdmax default pi>]]] \
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[solvent [<integer numwhb>]]
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\end{verbatim}
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\section{Selection}
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Analyses can be applied to a selection of solute atoms and solvent molecules.
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The selection is determined by
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\begin{verbatim}
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select ( [ super ] [ { <string atomlist> } ] |
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solvent <real range> | save <string filename> | read <string filename> )
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\end{verbatim}
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where {\rm \{atomlist\}} is the set of atom names selected from the specified residues.
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By default all solute atoms are selected. When keyword \verb+super+ is specified the selecion
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applies to the superimposition option.
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\par
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The selected atoms are specified by the string \verb+atomlist+ which
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takes the form
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\begin{verbatim}
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[{isgm [ - jsgm ] [,]} [:] [{aname[,]}]
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\end{verbatim}
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where \verb+isgm+ and \verb+jsgm+ are the first and last residue numbers,
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and \verb+aname+ is an atom name. In the atomname a question mark may be
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used as a wildcard character.
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For example, all protein backbone atoms are selected by
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\begin{verbatim}
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select _N,_CA,_C
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\end{verbatim}
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To select the backbone atoms in residues 20 to 80 and 90 to 100 only, use
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\begin{verbatim}
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select 20-80,90-100:_N,_CA,_C
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\end{verbatim}
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This selection is reset to apply to all atoms after each file
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directive.
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Solvent molecules within \verb+range+ nm from any selected solute atom
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are selected by
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\begin{verbatim}
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select solvent <real range>
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\end{verbatim}
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After solvent selection, the solute atom selection is reset to being all
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selected.
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The current selection can be saved to, or read from a file using the
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\verb+save+ and \verb+read+ keywords, respectively.
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\par
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Some analysis are performed on groups of atoms. These groups of atoms
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are defined by
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\begin{verbatim}
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define <integer igroup> [<real rsel>] [solvent] { <string atomlist> }
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\end{verbatim}
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The string atom in this definitions again takes the form
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\begin{verbatim}
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[{isgm [ - jsgm ] [,]} [:] [{aname[,]}]
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\end{verbatim}
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where \verb+isgm+ and \verb+jsgm+ are the first and last residue numbers,
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and \verb+aname+ is an atom name. In the atomname a question mark may be
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used as a wildcard character.
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Multiple define directive can be used to define a single set of atoms.
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\section{Coordinate analysis}
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To analyze the root mean square deviation from the specified reference
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coordinates:
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\begin{verbatim}
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rmsd
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\end{verbatim}
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To analyze protein $\phi$-$\psi$ and backbone hydrogen bonding:
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\begin{verbatim}
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ramachandran
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\end{verbatim}
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To define a distance:
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\begin{verbatim}
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distance <integer ibond> <string atomi> <string atomj>
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\end{verbatim}
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To define an angle:
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\begin{verbatim}
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angle <integer iangle> <string atomi> <string atomj> <string atomk>
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\end{verbatim}
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To define a torsion:
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\begin{verbatim}
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torsion <integer itorsion> <string atomi> <string atomj> \
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<string atomk> <string atoml>
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\end{verbatim}
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To define a vector:
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\begin{verbatim}
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vector <integer ivector> <string atomi> <string atomj>
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\end{verbatim}
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The atom string in these definitions takes the form
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\begin{verbatim}
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<integer segment>:<string atomname> | w<integer molecule>:<string atomname>
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\end{verbatim}
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for solute and solvent atom specification, respectively.
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To define charge distribution in z-direction:
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\begin{verbatim}
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charge_distribution <integer bins>
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\end{verbatim}
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Analyses on atoms in a predefined group are specified by
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\begin{verbatim}
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group [<integer igroup> [periodic <integer ipbc>] \
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( local [<real rsel default 0.0>] [<real rval default rsel>]
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<string function> )
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\end{verbatim}
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where \verb+igroup+ specifies the group of atoms defined with a
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\verb+define+ directive. Keyword \verb+periodic+ can be used to
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specify the periodicity, \verb+ipbc=1+ for periodicity in \verb+z+,
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\verb+ipbc=2+ for periodicity in \verb+x+ and \verb+y+, and
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\verb+ipbc=3+ for periodicity in \verb+x+, \verb+y+ and \verb+z+.
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Currently the only option is \verb+local+ which prints all selected
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solute atom with a distance between \verb+rsel+ and \verb+rval+ from
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the atoms defined in \verb+igroup+. The actual analysis is done by the
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\verb+scan+ deirective. A formatted report is printed from
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\verb+group+ analyses using
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\begin{verbatim}
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report <string filename> local
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\end{verbatim}
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Analyses on pairs of atoms in predefined groups are specified by
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\begin{verbatim}
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groups [<integer igroup> [<integer jgroup>]] [periodic [<integer ipbc default 3>]] \
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<string function> [<real value1> [<real value2>]] [<string filename>]
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\end{verbatim}
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where $igroup$ and $jgroup$ are groups of atoms defined with a
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\verb+define+ directive. Keyword \verb+periodic+ specifies that
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periodic boundary conditions need to be applied in $ipbc$ dimensions.
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The type of analysis is define by $function$, $value1$ and $value2$.
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If $filename$ is specified, the analysis is applied to the reference
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coordinates and written to the specified file. If no filename is
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given, the analysis is applied to the specified trajectory and
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performed as part of the \verb+scan+ directive.
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Implemented analyses defined by
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\verb+<string function> [<real value1> [<real value2>]]+ include\\
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\\
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\verb+distance+ to calculate the distance between the centers of geometry of the
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two specified groups of atoms, and\\
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\verb+distances+ to calculate all atomic distances between atoms
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in the specified groups that lie between $value1$ and $value2$.
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Coordinate histograms are specified by
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\begin{verbatim}
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histogram <integer idef> [<integer length>] zcoordinate <string filename>
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\end{verbatim}
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where $idef$ is the atom group definition number, $length$ is the size
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of the histogram, \verb+zcoordinate+ is the currently only histogram option,
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and $filename$ is the filname to which the histogram is written.
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Order parameters are evalated using
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\begin{verbatim}
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order <integer isel> <integer jsel> <string atomi> <string atomj>
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\end{verbatim}
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This is an experimental feature.
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To write the average coordinates of a trajectory
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\begin{verbatim}
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average [super] <string filename>
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\end{verbatim}
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To perform the coordinate analysis:
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\begin{verbatim}
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scan [ super ] <string filename>
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\end{verbatim}
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which will create, depending on the specified analysis options
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files filename.rms and filename.ana. After the scan directive
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previously defined coordinate analysis options are all reset.
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Optional keyword \verb+super+ specifies that frames read from
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the trajectory file(s) are superimposed to the reference structure
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before the analysis is performed.
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\section{Essential dynamics analysis}
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Essential dynamics analysis is performed by
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\begin{verbatim}
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essential
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\end{verbatim}
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This can be followed by one or more
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\begin{verbatim}
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project <integer vector> <string filename>
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\end{verbatim}
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to project the trajectory onto the specified vector. This will
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create files filename with extensions frm or trj, val, vec, \_min.pdb
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and \_max.pdb, with the projected trajectory, the projection
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value, the eigenvector, and the minimum and maximum projection
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structure.
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For example, an essential dynamics analysis with projection onto
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the first vector generating files firstvec.\{trj, val, vec, \_min.pdb, \_max.pdb\}
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is generated by
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\begin{verbatim}
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essential
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project 1 firstvec
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\end{verbatim}
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\section{Trajectory format conversion}
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To write a single frame in PDB or XYZ format, use
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\begin{verbatim}
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write [<integer number default 1>] [super] [solute] <string filename>
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\end{verbatim}
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To copy the selected frames from the specified trejctory file(s),
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onto a new file, use
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\begin{verbatim}
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copy [solute] [rotate <real tangle>] <string filename>
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\end{verbatim}
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To superimpose the selected atoms for each specified frame to the
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reference coordinates before copying onto a new file, use
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\begin{verbatim}
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super [solute] [rotate <real tangle>] <string filename>
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\end{verbatim}
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The \verb+rotate+ directive specifies that the structure will make
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a full ratation every tangle ps. This directive only has effect when
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writing povray files.
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The format of the new file is determined from the extension, which
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can be one of
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\begin{tabular}{rl}
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amb & \amber\ formatted trajectory file (obsolete)\\
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arc & \discover\ archive file\\
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bam & \amber\ unformatted trajectory file\\
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crd & \amber\ formatted trajectory file\\
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dcd & \charmm\ formatted trajectory file\\
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esp & \gopenmol\ formatted electrostatic potential files\\
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frm & \ecce\ frames file (obsolete)\\
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pov & \povray\ input files\\
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trj & \nwchem\ trajectory file\\
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\end{tabular}
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If no extension is specified, a {\rm trj} formatted file will be written.
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A special tag can be added to {\rm frm} and {\rm pov} formatted files using
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\begin{verbatim}
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label <integer itag> <string tag> [ <real rval default 1.0> ] \\
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[ <integer iatag> [ <integer jatag default iatag> ] [ <real rtag default 0.0> ] ]
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[ <string anam> ]
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\end{verbatim}
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where tag number $itag$ is set to the string $tag$ for all atoms
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anam within a distance $rtag$ from segments $iatag$ through $jatag$.
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A question mark can be used in anam as a wild card character.
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\par
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Atom rendering is specified using
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\begin{verbatim}
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render ( cpk | stick ) [ <real rval default 1.0> ] \\
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[ <integer iatag> [ <integer jatag default iatag> ] [ <real rtag default 0.0> ] ]
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[ <string anam> ]
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\end{verbatim}
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for all atoms anam within a distance $rtag$ from segments $iatag$ through $jatag$,
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and a scaling factor of $rval$. A question mark can be used in anam as a wild card
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character.
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\par
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Atom color is specified using
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\begin{verbatim}
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color ( <string color> | atom ) \\
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[ <integer iatag> [ <integer jatag default iatag> ] [ <real rtag default 0.0> ] ]
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[ <string anam> ]
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\end{verbatim}
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for all atoms anam within a distance $rtag$ from segments $iatag$ through $jatag$.
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A question mark can be used in anam as a wild card character.
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\par
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For example, to display all carbon atoms in segments 34 through 45
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in green and rendered cpk in povray files can be specified with
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\begin{verbatim}
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render cpk 34 45 _C??
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color green 34 45 _C??
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\end{verbatim}
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Coordinates written to a pov file can be scaled using
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\begin{verbatim}
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scale <real factor>
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\end{verbatim}
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A zero or negative scaling factor will scale the coordinates to
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lie within [-1,1] in all dimensions.
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\par
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The cpk rendering in povray files can be scaled by
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\begin{verbatim}
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cpk <real factor default 1.0>
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\end{verbatim}
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\par
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The stick rendering in povray files can be scaled by
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\begin{verbatim}
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stick <real factor default 1.0>
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\end{verbatim}
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The initial sequence number of esp related files is defined by
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\begin{verbatim}
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index <integer index default 1>
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\end{verbatim}
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A sequence of trajectory files with unequal lengths can be converted to files
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with all $nclean$ frames using
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\begin{verbatim}
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clean <integer nclean>
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\end{verbatim}
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\section{Electrostatic potentials}
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A file in plt format of the electrostatic potential resulting
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from partial charges generated by the ESP module is generated
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by the command
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\begin{verbatim}
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esp [ <integer spacing default 10> ] \
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[ <real rcut default 1.0> ] [periodic [<integer iper default 3>]] \
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[ <string xfile> [ <string pltfile> ] ]
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\end{verbatim}
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The input coordinates are taken from the {\rm xyzq} file that can
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be generated from a {\rm rst} by the prepare module. Parameter
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spacing specifies the number of gridpoints per nm, rcut specifies
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extent of the charge grid beyond the molecule.
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Periodic boundaries will be used if \verb+periodic+
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is specified. If \verb+iper+ is set to 2, periodic boundary
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conditions are applied in x and y dimensions only. If \verb+periodic+
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is specified, a negative value of \verb+rcut+ will extend the grid
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in the periodic dimensions by abs(\verb+rcut+), otherwise this value
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will be ignored in the periodic dimensions.
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The resulting {\rm plt} formatted file pltfile can be
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viewed with the gOpenMol program. The resulting electrostatic
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potential grid is in units of kJ\ mol$^{-1}$e$^{-1}$.
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If no files are specified, only the parameters are set. This
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analysis applies to solute(s) only.
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The electrostatic potential at specific point are evaluated using
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\begin{verbatim}
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esp_points [<string filpin> [<string filhol> [<string filpou> [<string filavg>]]]]
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\end{verbatim} |