145 lines
5.4 KiB
Plaintext
145 lines
5.4 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Commands_all.html)
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:line
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fix cmap command :h3
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[Syntax:]
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fix ID group-ID cmap filename :pre
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ID, group-ID are documented in "fix"_fix.html command
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cmap = style name of this fix command
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filename = force-field file with CMAP coefficients :ul
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[Examples:]
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fix myCMAP all cmap ../potentials/cmap36.data
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read_data proteinX.data fix myCMAP crossterm CMAP
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fix_modify myCMAP energy yes :pre
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[Description:]
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This command enables CMAP cross-terms to be added to simulations which
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use the CHARMM force field. These are relevant for any CHARMM model
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of a peptide or protein sequences that is 3 or more amino-acid
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residues long; see "(Buck)"_#Buck and "(Brooks)"_#Brooks2 for details,
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including the analytic energy expressions for CMAP interactions. The
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CMAP cross-terms add additional potential energy contributions to pairs
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of overlapping phi-psi dihedrals of amino-acids, which are important
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to properly represent their conformational behavior.
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The examples/cmap directory has a sample input script and data file
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for a small peptide, that illustrates use of the fix cmap command.
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As in the example above, this fix should be used before reading a data
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file that contains a listing of CMAP interactions. The {filename}
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specified should contain the CMAP parameters for a particular version
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of the CHARMM force field. Two such files are including in the
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lammps/potentials directory: charmm22.cmap and charmm36.cmap.
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The data file read by the "read_data" must contain the topology of all
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the CMAP interactions, similar to the topology data for bonds, angles,
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dihedrals, etc. Specially it should have a line like this
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in its header section:
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N crossterms :pre
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where N is the number of CMAP cross-terms. It should also have a section
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in the body of the data file like this with N lines:
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CMAP :pre
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1 1 8 10 12 18 20
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2 5 18 20 22 25 27
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\[...\]
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N 3 314 315 317 318 330 :pre
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The first column is an index from 1 to N to enumerate the CMAP terms;
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it is ignored by LAMMPS. The 2nd column is the "type" of the
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interaction; it is an index into the CMAP force field file. The
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remaining 5 columns are the atom IDs of the atoms in the two 4-atom
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dihedrals that overlap to create the CMAP 5-body interaction. Note
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that the "crossterm" and "CMAP" keywords for the header and body
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sections match those specified in the read_data command following the
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data file name; see the "read_data"_read_data.html doc page for
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more details.
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A data file containing CMAP cross-terms can be generated from a PDB
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file using the charmm2lammps.pl script in the tools/ch2lmp directory
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of the LAMMPS distribution. The script must be invoked with the
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optional "-cmap" flag to do this; see the tools/ch2lmp/README file for
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more information.
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The potential energy associated with CMAP interactions can be output
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as described below. It can also be included in the total potential
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energy of the system, as output by the
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"thermo_style"_thermo_style.html command, if the "fix_modify
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energy"_fix_modify.html command is used, as in the example above. See
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the note below about how to include the CMAP energy when performing an
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"energy minimization"_minimize.html.
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:line
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[Restart, fix_modify, output, run start/stop, minimize info:]
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This fix writes the list of CMAP cross-terms to "binary restart
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files"_restart.html. See the "read_restart"_read_restart.html command
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for info on how to re-specify a fix in an input script that reads a
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restart file, so that the operation of the fix continues in an
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uninterrupted fashion.
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The "fix_modify"_fix_modify.html {energy} option is supported by this
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fix to add the potential "energy" of the CMAP interactions system's
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potential energy as part of "thermodynamic output"_thermo_style.html.
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The "fix_modify"_fix_modify.html {virial} option is supported by this
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fix to add the contribution due to the interaction between atoms to
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the system's virial as part of "thermodynamic output"_thermo_style.html.
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The default is {virial yes}
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This fix computes a global scalar which can be accessed by various
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"output commands"_Howto_output.html. The scalar is the potential
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energy discussed above. The scalar value calculated by this fix is
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"extensive".
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No parameter of this fix can be used with the {start/stop} keywords of
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the "run"_run.html command.
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The forces due to this fix are imposed during an energy minimization,
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invoked by the "minimize"_minimize.html command.
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NOTE: If you want the potential energy associated with the CMAP terms
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forces to be included in the total potential energy of the system (the
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quantity being minimized), you MUST enable the
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"fix_modify"_fix_modify.html {energy} option for this fix.
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[Restrictions:]
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To function as expected this fix command must be issued {before} a
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"read_data"_read_data.html command but {after} a
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"read_restart"_read_restart.html command.
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This fix can only be used if LAMMPS was built with the MOLECULE
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package. See the "Build package"_Build_package.html doc page for more
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info.
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[Related commands:]
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"fix_modify"_fix_modify.html, "read_data"_read_data.html
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[Default:] none
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:line
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:link(Buck)
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[(Buck)] Buck, Bouguet-Bonnet, Pastor, MacKerell Jr., Biophys J, 90, L36
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(2006).
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:link(Brooks2)
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[(Brooks)] Brooks, Brooks, MacKerell Jr., J Comput Chem, 30, 1545 (2009).
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