From 7f4f74d396e758a09eeece6f6dcd2809b4c7033d Mon Sep 17 00:00:00 2001 From: Eric Bylaska Date: Wed, 9 Feb 2005 23:47:37 +0000 Subject: [PATCH] ... --- doc/user/qmmm.tex | 290 ++++++++++++++++++++++++++++++++++++---------- 1 file changed, 228 insertions(+), 62 deletions(-) diff --git a/doc/user/qmmm.tex b/doc/user/qmmm.tex index 1b3dfc2784..9b26f6f0d4 100644 --- a/doc/user/qmmm.tex +++ b/doc/user/qmmm.tex @@ -1,13 +1,13 @@ -% $Id: qmmm.tex,v 1.10 2003-04-11 14:10:05 d3j191 Exp $ +% $Id: qmmm.tex,v 1.11 2005-02-09 23:47:37 bylaska Exp $ \label{sec:qmmm} -Combined or hybrid Quantum Mechanics and Molecular Mechanics (QM/MM) +Combined or hybrid Quantum Mechanics and Molecular Mechanics (QMMM) is a simulation methodology that is about 15 years old but in all the literature there are cautions that calibration computations must be done to validate the model for each particular chemical system studied. This is not a black box style computation and the NWChem -users are advised that without calibration QM/MM may not give the +users are advised that without calibration QMMM may not give the appropriate results\footnote{c.f., Singh and Kollman, J. Comp. Chem. {\bf 7}, 718 (1986); M.~J.~Field, P.~A.~Bash and M.~Karplus, J. Comp. Chem. {\bf 11}, 700, (1990); J. Gao, ``Methods and @@ -15,100 +15,266 @@ appropriate results\footnote{c.f., Singh and Kollman, J. Comp. Chem. Potentials.'' In {\it Reviews in Computational Chemistry}; K.~B.~Lipkowitz, D.~B.~Boyd, Eds.; VCH Publishers: New York; Vol. 7, pp 119-185 (1995); and M. A. Thompson and G. K. Schenter, J. - Phys. Chem {\bf 99} 6374 (1995) }. + Phys. Chem {\bf 99} 6374 (1995) }. Since both quantum-mechanical and classical +molecular mechanics are involved in the calculation good working knowledge of the two methods +is required to ensure meaningful results. -The QM/MM module in NWChem is driven by the molecular dynamics module. -This module currently works for any QM method that has -analytic gradients\footnote{The QM/MM method will work with numerical - gradients available in NWChem, but it is expected that the - performance will not allow any substantive simulations}. The input -for this requires the definition of chemical system via the same -interface that is used by the MD module (c.f. Section -\ref{sec:nwmd}). The extensions to this interface include the -definition of ``Quantum'' atoms and ``Link'' where appropriate. The -QM information must be present in the traditional NWChem input deck -except for the geometry\footnote{Any geometry information in the - traditional form will be ignored}. The geometrical information will -be constructed automatically by nwmd. For dynamics and free energy -simulations the input is again identical to that for nwmd with -limitations on the kinds of simulations that can be done. -Link atoms are defined by the molecular dynamics module, based on -the specification of the quantum atoms in the prepare module. For -the link atoms, basis sets \verb+X_L+ need to be defined in the -basis set input block. - -The QM/MM module is invoked with the task directive where the -``theory'' is QMMM. The recognized operations on the QM/MM theory -directive are energy, optimize, and dynamics. +The QMMM module is invoked with the following task directive. \begin{verbatim} - task qmmm (energy | optimize | dynamics) + task qmmm [numerical] [ignore] +\end{verbatim} +where {\it qmtheory} specifies quantum method for the calculation of the quantum region. It is expected that +most of QMMM simulations will be performed with +with HF or DFT theories, but any other QM theory supported by NWChem should also work. +Currently the supported operations for QMMM runs +are energy, optimize, saddle, dynamics, numerical hessian, and numerical +frequencies. + + +Unlike pure +quantum mechanical calculations the information about the chemical system +for QMMM simulations is contained not in the geometry block but in the externally prepared topology and restart files. +These files have to be present prior to any QMMM simulation. +The input file for QMMM simulation can be divided into three major parts -- specification of the molecular +mechanics parameters for the classical region, specification of the quantum mechanical method for the quantum region, +and the parameters of the interaction between quantum and classical methods. +All this discussed in detail in the sections below. + +\section{Preparation of the restart and topology files} + +Generated by the prepare +module (see section \ref{sec:prepare}) restart and topology files contain +information about the classical force field as well as the +coordinates of quantum (qm) and molecular +mechanics (mm) regions. +In a typical setting this "preparation stage" +will be run separately from main QMMM simulation. This will require a +properly formatted +PDB file for the system. In more complex cases (e.g.non-standard residues or nucleotides) additional fragment and parameter +files might have to be provided by the user. The definition of the quantum region +in the input for the prepare module is specified by either {\it modify atom} directive (see Section \ref{sec:prepare}): + +\begin{verbatim} +modify atom : quantum \end{verbatim} -Tasks \verb+gradient+, \verb+saddle+, \verb+frequencies+ and -\verb+thermodynamics+ are currently not available in the QM/MM mode. +or {\it modify segment} directive + +\begin{verbatim} +modify segment quantum +\end{verbatim} + +Here {\it isgm} and {\it atomname} refer to the residue number and atom name record +as given in the PDB file. +It is important to note that +that the leading blanks +in atom name record should be indicated with underscores. +Per PDB format quidelines the atom name record starts at column 13. If, for example, +the atom name record "OW" starts +in the 14th column in PDB file, it will appear +as "\_OW" in the modify atom directive in the prepare block. In the current implementation +only solute atoms can be declared as quantum. If part of the solvent has to be treated quantum mechanically +then it has to redeclared to be solute. +In addition to modify commands the prepare input block should +also contain {\it update lists} and {\it ignore} directives. There are other options +that can be used in the input block for the prepare module ( e.g. solvating the structure, etc ), + those discussed +in more details in Section \ref{sec:prepare}. +The successful run of the prepare module will result in generation of +topology and restart files. Similar to classical MD, both files are required for QMMM simulations +and have to be placed in the same directory +as the input file. Here is an example input file that will generate QMMM restart and topology files for the ethanol molecule + +\begin{verbatim} +title "Prepare QMMM calculation of ethanol" +start etl + +prepare +#--name of the pdb file + source etl0.pdb +#--generate new topology and sequence file + new_top new_seq +#--generate new restart file + new_rst +#--define quantum region (note the use of underscore) + modify atom 1:_C1 quantum + modify atom 1:2H1 quantum + modify atom 1:3H1 quantum + modify atom 1:4H1 quantum +# + update lists + ignore +end +task prepare +\end{verbatim} + +These are contents of etl0.pdb file used in the above input file. +\begin{verbatim} +ATOM 1 O etl 1 1.201 -0.271 -0.000 1.00 0.00 O +ATOM 2 H etl 1 1.995 0.329 -0.000 1.00 0.00 H +ATOM 3 C1 etl 1 -1.180 -0.393 0.000 1.00 0.00 C +ATOM 4 2H1 etl 1 -2.128 0.155 -0.000 1.00 0.00 H +ATOM 5 3H1 etl 1 -1.130 -1.030 0.887 1.00 0.00 H +ATOM 6 4H1 etl 1 -1.130 -1.030 -0.887 1.00 0.00 H +ATOM 7 C2 etl 1 0.006 0.573 0.000 1.00 0.00 C +ATOM 8 2H2 etl 1 -0.042 1.220 0.890 1.00 0.00 H +ATOM 9 3H2 etl 1 -0.042 1.220 -0.890 1.00 0.00 H +END +\end{verbatim} + +Running the input shown above will produce (among other things) the topology file (etl.top) and the restart file +(etl{\_}md.rst). The naming of the topology file follows after the rtdb name specified in the start directive in the input (i.e. "start etl"), +while the "{\_}md" suffix in the restart file name is specific to the way prepare module works in this particular case. If necessary, this +particular naming scheme can be altered using {\it system} keyword in the prepare input block (for more details see Section \ref{sec:prepare}). + +\section{Molecular Mechanics Parameters} +The molecular mechanics parameters are given in the form of standard MD input block as +used by the MD module (c.f. Section \ref{sec:nwmd}). This input block +is required for QMMM simulations. It specifies the +restart and topology file that will be used in the calculation. +It also contains information relevant to the calculation +of the classical region +(e.g. cutoff distances, constraints, optimization and dynamics parameters, etc) +in the system. In this input block one can also set fixed atom constraints on both classical and quantum atoms. Continuing with our +example for ethanol molecule here is a simple input block that may be used for this system. + +\begin{verbatim} + md +# this specifies that etl_md.rst will be used as a restart file +# and etl.top will be a topology file + system etl_md +# if we ever wanted to fix C1 atom + fix solute 1 _C1 + end +\end{verbatim} -The QM/MM input consists of the standard NWChem input block: +\section{Quantum Mechanical Parameters} + +The parameters defining calculation of the QM region (including basis sets) +must be present in the traditional NWChem input format +except for the geometry block. The geometrical information will +be constructed automatically by QMMM using information from the MD module. + +\section{QMMM interface parameters} + +The QMMM interface parameters define the interaction between classical and quantum regions. +The input follows standard NWChem format: \begin{verbatim} qmmm - ... + [ eref ] + [ bqzone ] + [ bq_exclude <(none||all||linkbond||linkbond_H) default none>] + [ bq_update <(static||dynamic) >] + [ link_atoms <(hydrogen||halogen) default halogen>] + [ link_ecp <(auto||user) default auto>] + [ optimization <(all||mm|qm) default qm>] end \end{verbatim} -The \verb+qmmm+ has the following the additional sub-directive that the user -may specify for the particular simulation. These options currently are: +Detailed explanation of the subdirectives in the QMMM input block is given below: \begin{itemize} \item \begin{verbatim} -eatoms < real eatoms> + eref \end{verbatim} -There is one compound input directive that must exist for the QM/MM -simulation to proceed. This sets the relative zero of energy for the -QM component of the system. It is not incorrect to leave this value as -zero but the energetics of the QM system will likely over shadow the -MM component of the system. Properties based on energy fluctuations -of the system will be overly sensitive to the energy of the QM -component of the system. The zero of energy for the MM system is by +This directive sets the relative zero of energy for the +QM component of the system. The need for this directive +arizes from different definitions of zero energy for QM and MM methods. +Most QM methods define the zero of energy for the system as +vacuum. The zero of energy for the MM system is by definition of most parameterized force fields the separated atom -energy. The zero of energy for QM systems by definition of most QM -methods is the vacuum. The {\it a priori} determination of the -separated atom energy for a particular QM method is not well defined -and thus leads to a number of assumptions or guess work depending upon -the particular QM method being utilized. Therefor, the determination -of the QM separated atom energy (``eatoms'') is left to the user. -There is no default for this and the input {\bf must} be present for a -QM/MM simulation. +energy. Therefore in many cases the energetics of the QM system +will likely overshadow the +MM component of the system. This imbalance can be corrected by +suitably chosen value of {\it eref} \item \begin{verbatim} -qatoms < real qatoms> + bqzone \end{verbatim} -This input directive is used to specify the total charge on the set -of quantum atoms. +This directive defines the radius of the zone (in angstroms) around the quantum region +where classical residues/segments +will be allowed to interact with quantum region electrostatically. It should be noted +that classical atoms interacting with quantum region via bonded interactions are always +included in the bqzone (this is true even if bqzone is set to $0.0$). In addition, even if one atom +of a given charged group is in the bqzone (residues are typically treated as one charged group) then the whole +group will be included in the bqzone. + \item \begin{verbatim} -link hydrogen + bq_exclude <(none||all||linkbond||linkbond_H) default none> \end{verbatim} -This directive specified to use hydrogens as link atoms. The default -is to use the next group VII atom. +This directive operates in conjunction with bqzone keyword offering additional level of control +on electrostatic interactions between quantum and classical regions. Default value {\it none} will +leave bqzone unchanged, {\it all} will remove all atoms from the bqzone resulting in +no electrostatic interactions between +classical and quantum regions, +{\it linkbond} will result in the removal of all atoms that are connected to a quantum region +by at most two bonds, +{\it linkbond{\_}H} is similar to {\it linkbond} but will only remove hydrogen atoms. +If necccessary, further modifications of the electrostatic interactions can be achieved +using the prepare module{\ref{sec:prepare}}. \item \begin{verbatim} -nobq ( hydrogen | all | none ) + bq_update <(static||dynamic) +\end{verbatim} +This directive controls whether the bqzone stays fixed ({\it static}) or constantly +updated ({\it dynamic}) during the calculation. In most cases direct specification of this keyword +will not be necessary as its value will be set automatically based on the nature of the calculation. + +\item +\begin{verbatim} +link_atoms <(hydrogen||halogen) default halogen> \end{verbatim} -This directive specifies that hydrogen atoms, all atoms, or no atoms, -respectively, bonded to link atoms will carry a zero charge in the -QM part of the calculation. +This directive controls the treatment of bonds crossing the boundary between quantum and classical regions. +The use of {\it hydrogen } keyword will trigger truncation of such bonds with hydrogen link atoms. The position of the hydrogen +atom will be calculated from the coordinates of the quantum and classical atom of the truncated bond using the +following expression +\begin{displaymath} +\mathbf{R}_{hlink} = (1-g)\mathbf{R}_{quant} + g*\mathbf{R}_{class} +\end{displaymath} +where $g$ is the scale factor set at $0.709$ + +Setting link{\_}atoms to {\it halogen } will result in the modification of the {\it \underline{quantum}} +atom of the truncated bond to +to the fluoride atom. This fluoride atom will typically carry an effective core potential (ECP) basis set as specified +in {\it link{\_}ecp} directive. + +\item +\begin{verbatim} + link_ecp <(auto||user) default auto> +\end{verbatim} +This directive specifies ECP basis set on fluoride link atoms. If set to {\it auto } +the ECP basis set given by Zhang, Lee, Yang for 6-31G* basis.\footnote{Y. Zhang, T. Lee, and W. Yang, J. Chem. Phys. 110, 46 (1999)} +will be used. Strictly speaking, this implies the use of 6-31G* spherical basis as the main basis set. +If other choices are desired then keyword {\it user } should be used and ECP basis set should be entered separatelly +following the format given in +section \ref{sec:ecp}. +The name tag for fluoride link atoms is F{\_}L. + +\item +\begin{verbatim} +optimization <(all||mm|qm) default qm> +\end{verbatim} + +This directive specifies which region will be optimized during qmmm optimization. If set to {\it all} both qm and mm +region will be optimized simultaneously using mm optimization module, if {\it mm} only mm portion will be optimized +using mm optimization module, finally if {\it qm} is specified then only qm region will be optimized using driver +module. + + \end{itemize} -All other parameters that control the QM/MM simulation are set via the -input to nwmd (see chapter \ref{sec:nwmd}). + +