Loading doc/src/Manual.txt +2 −2 Original line number Diff line number Diff line <!-- HTML_ONLY --> <HEAD> <TITLE>LAMMPS Users Manual</TITLE> <META NAME="docnumber" CONTENT="21 Sep 2016 version"> <META NAME="docnumber" CONTENT="26 Sep 2016 version"> <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories"> <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License."> </HEAD> Loading @@ -21,7 +21,7 @@ <H1></H1> LAMMPS Documentation :c,h3 21 Sep 2016 version :c,h4 26 Sep 2016 version :c,h4 Version info: :h4 Loading doc/src/Section_commands.txt +1 −0 Original line number Diff line number Diff line Loading @@ -501,6 +501,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "bond/create"_fix_bond_create.html, "bond/swap"_fix_bond_swap.html, "box/relax"_fix_box_relax.html, "cmap"_fix_cmap.html, "controller"_fix_controller.html, "deform (k)"_fix_deform.html, "deposit"_fix_deposit.html, Loading doc/src/Section_tools.txt +4 −3 Original line number Diff line number Diff line Loading @@ -107,9 +107,10 @@ The ch2lmp sub-directory contains tools for converting files back-and-forth between the CHARMM MD code and LAMMPS. They are intended to make it easy to use CHARMM as a builder and as a post-processor for LAMMPS. Using charmm2lammps.pl, you can convert an ensemble built in CHARMM into its LAMMPS equivalent. Using lammps2pdb.pl you can convert LAMMPS atom dumps into pdb files. post-processor for LAMMPS. Using charmm2lammps.pl, you can convert a PDB file with associated CHARMM info, including CHARMM force field data, into its LAMMPS equivalent. Using lammps2pdb.pl you can convert LAMMPS atom dumps into PDB files. See the README file in the ch2lmp sub-directory for more information. Loading doc/src/fix_cmap.txt 0 → 100644 +132 −0 Original line number Diff line number Diff line "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"_doc/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 (which it is by default). 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 (Buck) Buck, Bouguet-Bonnet, Pastor, MacKerell Jr., Biophys J, 90, L36 (2006). (Brooks) Brooks, Brooks, MacKerell Jr., J Comput Chem, 30, 1545 (2009). examples/README +1 −0 Original line number Diff line number Diff line Loading @@ -61,6 +61,7 @@ sub-directories: accelerate: use of all the various accelerator packages balance: dynamic load balancing, 2d system body: body particles, 2d system cmap: CMAP 5-body contributions to CHARMM force field colloid: big colloid particles in a small particle solvent, 2d system coreshell: adiabatic core/shell model comb: models using the COMB potential Loading Loading
doc/src/Manual.txt +2 −2 Original line number Diff line number Diff line <!-- HTML_ONLY --> <HEAD> <TITLE>LAMMPS Users Manual</TITLE> <META NAME="docnumber" CONTENT="21 Sep 2016 version"> <META NAME="docnumber" CONTENT="26 Sep 2016 version"> <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories"> <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License."> </HEAD> Loading @@ -21,7 +21,7 @@ <H1></H1> LAMMPS Documentation :c,h3 21 Sep 2016 version :c,h4 26 Sep 2016 version :c,h4 Version info: :h4 Loading
doc/src/Section_commands.txt +1 −0 Original line number Diff line number Diff line Loading @@ -501,6 +501,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "bond/create"_fix_bond_create.html, "bond/swap"_fix_bond_swap.html, "box/relax"_fix_box_relax.html, "cmap"_fix_cmap.html, "controller"_fix_controller.html, "deform (k)"_fix_deform.html, "deposit"_fix_deposit.html, Loading
doc/src/Section_tools.txt +4 −3 Original line number Diff line number Diff line Loading @@ -107,9 +107,10 @@ The ch2lmp sub-directory contains tools for converting files back-and-forth between the CHARMM MD code and LAMMPS. They are intended to make it easy to use CHARMM as a builder and as a post-processor for LAMMPS. Using charmm2lammps.pl, you can convert an ensemble built in CHARMM into its LAMMPS equivalent. Using lammps2pdb.pl you can convert LAMMPS atom dumps into pdb files. post-processor for LAMMPS. Using charmm2lammps.pl, you can convert a PDB file with associated CHARMM info, including CHARMM force field data, into its LAMMPS equivalent. Using lammps2pdb.pl you can convert LAMMPS atom dumps into PDB files. See the README file in the ch2lmp sub-directory for more information. Loading
doc/src/fix_cmap.txt 0 → 100644 +132 −0 Original line number Diff line number Diff line "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"_doc/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 (which it is by default). 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 (Buck) Buck, Bouguet-Bonnet, Pastor, MacKerell Jr., Biophys J, 90, L36 (2006). (Brooks) Brooks, Brooks, MacKerell Jr., J Comput Chem, 30, 1545 (2009).
examples/README +1 −0 Original line number Diff line number Diff line Loading @@ -61,6 +61,7 @@ sub-directories: accelerate: use of all the various accelerator packages balance: dynamic load balancing, 2d system body: body particles, 2d system cmap: CMAP 5-body contributions to CHARMM force field colloid: big colloid particles in a small particle solvent, 2d system coreshell: adiabatic core/shell model comb: models using the COMB potential Loading
