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sjplimp 2013-06-27 22:45:24 +00:00
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@ -44,30 +44,38 @@ module library which allows to calculate potentials of mean force
(PMFs) for any set of colvars, using different sampling methods:
currently implemented are the Adaptive Biasing Force (ABF) method,
metadynamics, Steered Molecular Dynamics (SMD) and Umbrella Sampling
(US) via a flexible harmonic restraint bias. This documentation
describes only the colvars fix itself and LAMMPS specific parts of the
code. The documentation of the colvars implementation itself is
available as part of the <A HREF = "http://www.ks.uiuc.edu/Research/namd/2.8/ug/node53.html">NAMD online
documentation</A>
(US) via a flexible harmonic restraint bias. The colvars library is
hosted at <A HREF = "http://colvars.github.io/">http://colvars.github.io/</A>
</P>
<P>There are example scripts for using this package with LAMMPS in
examples/USER/colvars.
<P>This documentation describes only the fix colvars command itself and
LAMMPS specific parts of the code. The full documentation of the
colvars library is available as <A HREF = "PDF/colvars-refman-lammps.pdf">this supplementary PDF document</A>
</P>
<P>The implementation of the portable collective variable library is also
documented in <A HREF = "#Henin">(Henin)</A>
<P>A detailed discussion of the implementation of the portable collective
variable library is in <A HREF = "#Fiorin">(Fiorin)</A>. Additional information can
be found in <A HREF = "#Henin">(Henin)</A>.
</P>
<P>There are some example scripts for using this package with LAMMPS in the
examples/USER/colvars directory.
</P>
<HR>
<P>The only mandatory argument to the fix is the filename to the colvars
input file that contains all input that is independent from the MD
input file that contains the input that is independent from the MD
program in which the colvars library has been integrated.
</P>
<P>The <I>group-ID</I> entry is ignored. The collective variable module will
always apply to the entire system, i.e. use the group <I>all</I>.
always apply to the entire system and there can only be one instance
of the colvars fix at a time. The colvars fix will only communicate
the minimum information necessary and the colvars library supports
multiple, completely independent collective variables, so there is
no restriction to functionaliry by limiting the number of colvars fixes.
</P>
<P>The <I>input</I> keyword allows to specify a state file that would contain
the information required in order to continue a calculation, e.g.
from a restart. Setting it to NULL will start a new colvars run.
the restart information required in order to continue a calculation from
a prerecorded state. Fix colvars records it state in <A HREF = "restart.html">binary restart</A>
files, so when using the <A HREF = "read_restart.html">read_restart</A> command,
this is usually not needed.
</P>
<P>The <I>output</I> keyword allows to specify the output prefix. All output
files generated will use this prefix followed by the ".colvars." and
@ -90,8 +98,10 @@ temperature.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>.
<P>This fix writes the current status of the colvars module into
<A HREF = "restart.html">binary restart files</A>. This is in addition to the text
mode status file that is written by the colvars module itself and the
kind of information in both files is identical.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the energy change from the biasing force added by the fix
@ -109,10 +119,10 @@ calculated by this fix is "extensive".
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>There can only be one colvars fix active at a time. Since the
colvars module itself can handle an arbitrary number of collective
variables and always applies to the entire system, this is not
really a deficit in practice.
<P>There can only be one colvars fix active at a time. Since the interface
communicates only the minimum amount of information and colvars module
itself can handle an arbitrary number of collective variables, this is
not a limitation of functionality.
</P>
<P><B>Related commands:</B>
</P>
@ -125,9 +135,13 @@ and tstat = NULL.
</P>
<HR>
<A NAME = "Fiorin"></A>
<P><B>(Fiorin)</B> Fiorin , Klein, Henin, Mol. Phys., DOI:10.1080/00268976.2013.813594
</P>
<A NAME = "Henin"></A>
<P><B>(Henin)</B> Hénin, Fiorin, Chipot, Klein, J. Chem. Theory Comput., 6,
<P><B>(Henin)</B> Henin, Fiorin, Chipot, Klein, J. Chem. Theory Comput., 6,
35-47 (2010)
</P>
</HTML>

53
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@ -36,30 +36,38 @@ module library which allows to calculate potentials of mean force
(PMFs) for any set of colvars, using different sampling methods:
currently implemented are the Adaptive Biasing Force (ABF) method,
metadynamics, Steered Molecular Dynamics (SMD) and Umbrella Sampling
(US) via a flexible harmonic restraint bias. This documentation
describes only the colvars fix itself and LAMMPS specific parts of the
code. The documentation of the colvars implementation itself is
available as part of the "NAMD online
documentation"_http://www.ks.uiuc.edu/Research/namd/2.8/ug/node53.html
(US) via a flexible harmonic restraint bias. The colvars library is
hosted at "http://colvars.github.io/"_http://colvars.github.io/
There are example scripts for using this package with LAMMPS in
examples/USER/colvars.
This documentation describes only the fix colvars command itself and
LAMMPS specific parts of the code. The full documentation of the
colvars library is available as "this supplementary PDF document"_PDF/colvars-refman-lammps.pdf
The implementation of the portable collective variable library is also
documented in "(Henin)"_#Henin
A detailed discussion of the implementation of the portable collective
variable library is in "(Fiorin)"_#Fiorin. Additional information can
be found in "(Henin)"_#Henin.
There are some example scripts for using this package with LAMMPS in the
examples/USER/colvars directory.
:line
The only mandatory argument to the fix is the filename to the colvars
input file that contains all input that is independent from the MD
input file that contains the input that is independent from the MD
program in which the colvars library has been integrated.
The {group-ID} entry is ignored. The collective variable module will
always apply to the entire system, i.e. use the group {all}.
always apply to the entire system and there can only be one instance
of the colvars fix at a time. The colvars fix will only communicate
the minimum information necessary and the colvars library supports
multiple, completely independent collective variables, so there is
no restriction to functionaliry by limiting the number of colvars fixes.
The {input} keyword allows to specify a state file that would contain
the information required in order to continue a calculation, e.g.
from a restart. Setting it to NULL will start a new colvars run.
the restart information required in order to continue a calculation from
a prerecorded state. Fix colvars records it state in "binary restart"_restart.html
files, so when using the "read_restart"_read_restart.html command,
this is usually not needed.
The {output} keyword allows to specify the output prefix. All output
files generated will use this prefix followed by the ".colvars." and
@ -82,8 +90,10 @@ temperature.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html.
This fix writes the current status of the colvars module into
"binary restart files"_restart.html. This is in addition to the text
mode status file that is written by the colvars module itself and the
kind of information in both files is identical.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy change from the biasing force added by the fix
@ -101,10 +111,10 @@ This fix is part of the USER-COLVARS package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
There can only be one colvars fix active at a time. Since the
colvars module itself can handle an arbitrary number of collective
variables and always applies to the entire system, this is not
really a deficit in practice.
There can only be one colvars fix active at a time. Since the interface
communicates only the minimum amount of information and colvars module
itself can handle an arbitrary number of collective variables, this is
not a limitation of functionality.
[Related commands:]
@ -117,7 +127,10 @@ and tstat = NULL.
:line
:link(Fiorin)
[(Fiorin)] Fiorin , Klein, Henin, Mol. Phys., DOI:10.1080/00268976.2013.813594
:link(Henin)
[(Henin)] Hénin, Fiorin, Chipot, Klein, J. Chem. Theory Comput., 6,
[(Henin)] Henin, Fiorin, Chipot, Klein, J. Chem. Theory Comput., 6,
35-47 (2010)

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@ -0,0 +1,58 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>group2ndx command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>group2ndx file group-ID ...
</PRE>
<UL><LI>file = name of index file to write out
<LI>zero or more group IDs may be appended
</UL>
<P><B>Examples:</B>
</P>
<PRE>group2ndx allindex.ndx
group2ndx someindex.ndx upper lower mobile
</PRE>
<P><B>Description:</B>
</P>
<P>Write a Gromacs style index file in text format that associates atom IDs
with the corresponding group definitions. This index file can be used
with in combination with Gromacs analysis tools or to import group
definitions into the <A HREF = "fix_colvars.html">fix colvars</A> input file.
</P>
<P>Without specifying any group IDs, all groups will be written to the index
file. When specifying group IDs, only those groups will be written to the
index file. In order to follow the Gromacs conventions, the group <I>all</I>
will be renamed to <I>System</I> in the index file.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>This command requires that atoms have atom IDs, since this is the
information that is written to the index file.
</P>
<P>This fix is part of the USER-COLVARS package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "group.html">group</A>, <A HREF = "dump.html">dump</A>, <A HREF = "fix_colvars.html">fix colvars</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

51
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@ -0,0 +1,51 @@
"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
group2ndx command :h3
[Syntax:]
group2ndx file group-ID ... :pre
file = name of index file to write out :ulb,l
zero or more group IDs may be appended :l
:ule
[Examples:]
group2ndx allindex.ndx
group2ndx someindex.ndx upper lower mobile :pre
[Description:]
Write a Gromacs style index file in text format that associates atom IDs
with the corresponding group definitions. This index file can be used
with in combination with Gromacs analysis tools or to import group
definitions into the "fix colvars"_fix_colvars.html input file.
Without specifying any group IDs, all groups will be written to the index
file. When specifying group IDs, only those groups will be written to the
index file. In order to follow the Gromacs conventions, the group {all}
will be renamed to {System} in the index file.
:line
[Restrictions:]
This command requires that atoms have atom IDs, since this is the
information that is written to the index file.
This fix is part of the USER-COLVARS package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"group"_group.html, "dump"_dump.html, "fix colvars"_fix_colvars.html
[Default:] none