# fix cmap command ## Syntax fix ID group-ID cmap filename - ID, group-ID are documented in [fix](fix) command - cmap = style name of this fix command - filename = force-field file with CMAP coefficients ## Examples ``` LAMMPS 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 5-body interactions 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)](Buck) and [(Brooks)](Brooks2) for details, including the analytic energy expressions for CMAP interactions. The CMAP 5-body 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 5-body interactions. 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 5-atom tuples; 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 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](read_data) page for more details. A data file containing CMAP 5-body interactions 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 same conversion script also creates the file of CMAP coefficient data which is read by this command. 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](thermo_style) command, if the [fix_modify energy](fix_modify) command is used, as in the example above. See the note below about how to include the CMAP energy when performing an [energy minimization](minimize). ------------------------------------------------------------------------ ## Restart, fix_modify, output, run start/stop, minimize info This fix writes the list of CMAP cross-terms to [binary restart files](restart). See the [read_restart](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](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](thermo_style) or output by the [compute pe/atom](compute_pe_atom) command. The default setting for this fix is [fix_modify energy yes](fix_modify). The [fix_modify](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](compute_pressure) and [compute stress/atom](compute_stress_atom) commands. The former can be accessed by [thermodynamic output](thermo_style). The default setting for this fix is [fix_modify virial yes](fix_modify). This fix computes a global scalar which can be accessed by various [output commands](Howto_output). 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](run) command. The forces due to this fix are imposed during an energy minimization, invoked by the [minimize](minimize) command. The [fix_modify](fix_modify) *respa* option is supported by this fix. This allows to set at which level of the [r-RESPA](run_style) integrator the fix is adding its forces. Default is the outermost level. :::: note ::: title Note ::: For energy minimization, 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](fix_modify) *energy* option for this fix. :::: ## Restrictions To function as expected this fix command must be issued *before* a [read_data](read_data) command but *after* a [read_restart](read_restart) command. This fix can only be used if LAMMPS was built with the MOLECULE package. See the [Build package](Build_package) page for more info. ## Related commands [fix_modify](fix_modify), [read_data](read_data) ## Default none ------------------------------------------------------------------------ ::: {#Buck} **(Buck)** Buck, Bouguet-Bonnet, Pastor, MacKerell Jr., Biophys J, 90, L36 (2006). ::: ::: {#Brooks2} **(Brooks)** Brooks, Brooks, MacKerell Jr., J Comput Chem, 30, 1545 (2009). :::