fix cmap command

Syntax

fix ID group-ID cmap filename

  • ID, group-ID are documented in fix command

  • cmap = style name of this fix command

  • filename = force-field file with CMAP coefficients

Examples

fix            myCMAP all cmap ../potentials/cmap36.data
read_data      proteinX.data fix myCMAP crossterm CMAP
fix_modify     myCMAP energy yes

Description

This command enables CMAP cross-terms to be added to simulations which use the CHARMM force field. These are relevant for any CHARMM model of a peptide or protein sequences that is 3 or more amino-acid residues long; see (Buck) and (Brooks) for details, including the analytic energy expressions for CMAP interactions. The CMAP cross-terms add additional potential energy contributions to pairs of overlapping phi-psi dihedrals of amino-acids, which are important to properly represent their conformational behavior.

The examples/cmap directory has a sample input script and data file for a small peptide, that illustrates use of the fix cmap command.

As in the example above, this fix should be used before reading a data file that contains a listing of CMAP interactions. The filename specified should contain the CMAP parameters for a particular version of the CHARMM force field. Two such files are including in the lammps/potentials directory: charmm22.cmap and charmm36.cmap.

The data file read by the “read_data” must contain the topology of all the CMAP interactions, similar to the topology data for bonds, angles, dihedrals, etc. Specially it should have a line like this in its header section:

N crossterms

where N is the number of CMAP cross-terms. It should also have a section in the body of the data file like this with N lines:

CMAP

       1       1       8      10      12      18      20
       2       5      18      20      22      25      27
       [...]
       N       3     314     315     317      318    330

The first column is an index from 1 to N to enumerate the CMAP terms; it is ignored by LAMMPS. The second column is the “type” of the interaction; it is an index into the CMAP force field file. The remaining 5 columns are the atom IDs of the atoms in the two 4-atom dihedrals that overlap to create the CMAP 5-body interaction. Note that the “crossterm” and “CMAP” keywords for the header and body sections match those specified in the read_data command following the data file name; see the read_data page for more details.

A data file containing CMAP cross-terms can be generated from a PDB file using the charmm2lammps.pl script in the tools/ch2lmp directory of the LAMMPS distribution. The script must be invoked with the optional “-cmap” flag to do this; see the tools/ch2lmp/README file for more information.

The potential energy associated with CMAP interactions can be output as described below. It can also be included in the total potential energy of the system, as output by the thermo_style command, if the fix_modify energy command is used, as in the example above. See the note below about how to include the CMAP energy when performing an energy minimization.

Restart, fix_modify, output, run start/stop, minimize info

This fix writes the list of CMAP cross-terms to binary restart files. See the read_restart command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion.

The fix_modify energy option is supported by this fix to add the potential energy of the CMAP interactions to both the global potential energy and peratom potential energies of the system as part of thermodynamic output or output by the compute pe/atom command. The default setting for this fix is fix_modify energy yes.

The fix_modify virial option is supported by this fix to add the contribution due to the CMAP interactions to both the global pressure and per-atom stress of the system via the compute pressure and compute stress/atom commands. The former can be accessed by thermodynamic output. The default setting for this fix is fix_modify virial yes.

This fix computes a global scalar which can be accessed by various output commands. The scalar is the potential energy discussed above. The scalar value calculated by this fix is “extensive”.

No parameter of this fix can be used with the start/stop keywords of the run command.

The forces due to this fix are imposed during an energy minimization, invoked by the minimize command.

The fix_modify respa option is supported by this fix. This allows to set at which level of the r-RESPA integrator the fix is adding its forces. Default is the outermost level.

Note

If you want the potential energy associated with the CMAP terms forces to be included in the total potential energy of the system (the quantity being minimized), you MUST not disable the fix_modify energy option for this fix.

Restrictions

To function as expected this fix command must be issued before a read_data command but after a read_restart command.

This fix can only be used if LAMMPS was built with the MOLECULE package. See the Build package page for more info.

Default

none

(Buck) Buck, Bouguet-Bonnet, Pastor, MacKerell Jr., Biophys J, 90, L36 (2006).

(Brooks) Brooks, Brooks, MacKerell Jr., J Comput Chem, 30, 1545 (2009).