forked from lijiext/lammps
65 lines
2.1 KiB
Plaintext
65 lines
2.1 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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group2ndx command :h3
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ndx2group command :h3
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[Syntax:]
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group2ndx file group-ID ...
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ndx2group file group-ID ... :pre
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file = name of index file to write out or read in :ulb,l
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zero or more group IDs may be appended :l
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:ule
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[Examples:]
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group2ndx allindex.ndx
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group2ndx someindex.ndx upper lower mobile
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ndx2group someindex.ndx
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ndx2group someindex.ndx mobile :pre
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[Description:]
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Write or read a Gromacs style index file in text format that associates
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atom IDs with the corresponding group definitions. This index file can be
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used with in combination with Gromacs analysis tools or to import group
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definitions into the "fix colvars"_fix_colvars.html input file. It can
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also be used to save and restore group definitions for static groups.
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The {group2ndx} command will write group definitions to an index file.
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Without specifying any group IDs, all groups will be written to the index
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file. When specifying group IDs, only those groups will be written to the
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index file. In order to follow the Gromacs conventions, the group {all}
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will be renamed to {System} in the index file.
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The {ndx2group} command will create of update group definitions from those
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stored in an index file. Without specifying any group IDs, all groups except
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{System} will be read from the index file and the corresponding groups
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recreated. If a group of the same name already exists, it will be completely
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reset. When specifying group IDs, those groups, if present, will be read
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from the index file and restored.
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:line
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[Restrictions:]
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This command requires that atoms have atom IDs, since this is the
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information that is written to the index file.
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These commands are part of the USER-COLVARS package. They are only
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enabled if LAMMPS was built with that package. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info.
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[Related commands:]
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"group"_group.html, "dump"_dump.html, "fix colvars"_fix_colvars.html
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[Default:] none
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