173 lines
5.6 KiB
ReStructuredText
173 lines
5.6 KiB
ReStructuredText
.. index:: fix cmap
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fix cmap command
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================
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Syntax
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""""""
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.. parsed-literal::
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fix ID group-ID cmap filename
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* cmap = style name of this fix command
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* filename = force-field file with CMAP coefficients
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Examples
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""""""""
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.. parsed-literal::
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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
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Description
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"""""""""""
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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 :ref:`(Buck) <Buck>` and :ref:`(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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.. parsed-literal::
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N crossterms
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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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.. parsed-literal::
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CMAP
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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
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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 :doc:`read\_data <read_data>` 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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:doc:`thermo\_style <thermo_style>` command, if the :doc:`fix\_modify energy <fix_modify>` 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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:doc:`energy minimization <minimize>`.
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----------
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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 :doc:`binary restart files <restart>`. See the :doc:`read\_restart <read_restart>` 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 :doc:`fix\_modify <fix_modify>` *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 :doc:`thermodynamic output <thermo_style>`.
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The :doc:`fix\_modify <fix_modify>` *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 :doc:`thermodynamic output <thermo_style>`.
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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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:doc:`output commands <Howto_output>`. 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 :doc:`run <run>` command.
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The forces due to this fix are imposed during an energy minimization,
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invoked by the :doc:`minimize <minimize>` command.
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.. note::
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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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:doc:`fix\_modify <fix_modify>` *energy* option for this fix.
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Restrictions
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""""""""""""
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To function as expected this fix command must be issued *before* a
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:doc:`read\_data <read_data>` command but *after* a
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:doc:`read\_restart <read_restart>` 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 :doc:`Build package <Build_package>` doc page for more
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info.
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Related commands
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""""""""""""""""
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:doc:`fix\_modify <fix_modify>`, :doc:`read\_data <read_data>`
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**Default:** none
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----------
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.. _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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.. _Brooks2:
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**(Brooks)** Brooks, Brooks, MacKerell Jr., J Comput Chem, 30, 1545 (2009).
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Commands_all.html
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