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CSG_MAP(1) General Commands Manual CSG_MAP(1) NAME csg_map - Part of the VOTCA package SYNOPSIS csg_map [OPTIONS] csg_map [--help] DESCRIPTION Convert a reference atomistic trajectory or configuration into a coarse- grained one based on a mapping xml-file. The mapping can be applied to ei- ther an entire trajectory or a selected set of frames only (see options). * csg_map --top FA-topol.tpr --trj FA-traj.trr --out CG-traj.xtc --cg cg- map.xml * csg_map --top FA-topol.tpr --trj FA-conf.gro --out CG-conf.gro --cg cg- map.xml * csg_map --top FA-topol.tpr --trj FA-traj.xtc --out FA-history.dlph --no-map * csg_map --top FA-field.dlpf --trj FA-history.dlph --out CG-history.dlph --cg cg-map.xml * csg_map --top .dlpf --trj .dlph --out .dlph --cg cg-map.xml convert HISTORY to HISTORY_CGV OPTIONS Allowed options: -h [ --help ] display this help and exit --verbose be loud and noisy --verbose1 be very loud and noisy -v [ --verbose2 ] be extremly loud and noisy --top arg atomistic topology file --out arg output file for coarse-grained trajectory --vel Write mapped velocities (if available) --force Write mapped forces (if available) --hybrid Create hybrid trajectory containing both atomistic and coarse-grained Mapping options: --cg arg coarse graining mapping and bond definitions (xml-file) --map-ignore arg list of molecules to ignore separated by ; --no-map disable mapping and act on original trajec- tory Trajectory options: --trj arg atomistic trajectory file --begin arg (=0) skip frames before this time (only works for Gromacs files) --first-frame arg (=0) start with this frame --nframes arg process the given number of frames AUTHORS Written and maintained by the VOTCA Development Team <devs@votca.org> COPYRIGHT Copyright 2009-2024 The VOTCA Development Team (http://www.votca.org) Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software dis- tributed under the License is distributed on an "AS IS" BASIS, WITHOUT WAR- RANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limi- tations under the License. VOTCA Development Team csg_map User Manual CSG_MAP(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | AUTHORS | COPYRIGHT
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