133 lines
4.8 KiB
Plaintext
133 lines
4.8 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
|
|
|
:link(lws,http://lammps.sandia.gov)
|
|
:link(ld,Manual.html)
|
|
:link(lc,Section_commands.html#comm)
|
|
|
|
:line
|
|
|
|
fix cmap command :h3
|
|
|
|
[Syntax:]
|
|
|
|
fix ID group-ID cmap filename :pre
|
|
|
|
ID, group-ID are documented in "fix"_fix.html command
|
|
cmap = style name of this fix command
|
|
filename = force-field file with CMAP coefficients :ul
|
|
|
|
[Examples:]
|
|
|
|
fix myCMAP all cmap ../potentials/cmap36.data
|
|
read_data proteinX.data fix myCMAP crossterm CMAP
|
|
fix_modify myCMAP energy yes :pre
|
|
|
|
[Description:]
|
|
|
|
This command enables CMAP crossterms 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)"_#Brooks for details,
|
|
including the analytic energy expressions for CMAP interactions. The
|
|
CMAP crossterms 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. Specically it should have a line like this
|
|
in its header section:
|
|
|
|
N crossterms :pre
|
|
|
|
where N is the number of CMAP crossterms. It should also have a section
|
|
in the body of the data file like this with N lines:
|
|
|
|
CMAP :pre
|
|
|
|
1 1 8 10 12 18 20
|
|
2 5 18 20 22 25 27
|
|
\[...\]
|
|
N 3 314 315 317 318 330 :pre
|
|
|
|
The first column is an index from 1 to N to enumerate the CMAP terms;
|
|
it is ignored by LAMMPS. The 2nd 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"_read_data.html doc page for
|
|
more details.
|
|
|
|
A data file containing CMAP crossterms 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"_thermo_style.html command, if the "fix_modify
|
|
energy"_fix_modify.html 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.html.
|
|
|
|
:line
|
|
|
|
[Restart, fix_modify, output, run start/stop, minimize info:]
|
|
|
|
No information about this fix is written to "binary restart
|
|
files"_restart.html.
|
|
|
|
The "fix_modify"_fix_modify.html {energy} option is supported by this
|
|
fix to add the potential "energy" of the CMAP interactions system's
|
|
potential energy as part of "thermodynamic output"_thermo_style.html.
|
|
|
|
This fix computes a global scalar which can be accessed by various
|
|
"output commands"_Section_howto.html#howto_15. 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.html command.
|
|
|
|
The forces due to this fix are imposed during an energy minimization,
|
|
invoked by the "minimize"_minimize.html command.
|
|
|
|
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 enable the
|
|
"fix_modify"_fix_modify.html {energy} option for this fix.
|
|
|
|
[Restrictions:]
|
|
|
|
This fix can only be used if LAMMPS was built with the MOLECULE
|
|
package. See the "Making
|
|
LAMMPS"_Section_start.html#start_3 section for more info on packages.
|
|
|
|
[Related commands:]
|
|
|
|
"fix_modify"_fix_modify.html, "read_data"_read_data.html
|
|
|
|
[Default:] none
|
|
|
|
:line
|
|
|
|
:link(Buck)
|
|
[(Buck)] Buck, Bouguet-Bonnet, Pastor, MacKerell Jr., Biophys J, 90, L36
|
|
(2006).
|
|
|
|
:link(Brooks)
|
|
[(Brooks)] Brooks, Brooks, MacKerell Jr., J Comput Chem, 30, 1545 (2009).
|