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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9786 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2013-04-23 19:04:04 +00:00
parent f1c64db6a9
commit 3dadc962c0
2 changed files with 20 additions and 2 deletions
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11
doc/fix_colvars.html
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@ -26,13 +26,15 @@
<PRE> <I>input</I> arg = colvars.state file name or prefix or NULL (default: NULL)
<I>output</I> arg = output filename prefix (default: out)
<I>seed</I> arg = seed for random number generator (default: 1966)
<I>unwrap</I> arg = <I>yes</I> or <I>no</I>
use unwrapped coordinates in collective variables (default: no)
<I>tstat</I> arg = fix id of a thermostat or NULL (default: NULL)
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix colvars peptide peptide.colvars.inp seed 2122 input peptide.colvars.state output peptide
<PRE>fix colvars peptide peptide.colvars.inp seed 2122 input peptide.colvars.state output peptide unwrap yes
fix colvars all colvars.inp
</PRE>
<P><B>Description:</B>
@ -74,6 +76,13 @@ a word like "state" or "traj".
<P>The <I>seed</I> keyword contains the seed for the random number generator
that will be used in the colvars module.
</P>
<P>The <I>unwrap</I> keyword controls whether wrapped or unwrapped coordinates
are passed to the colvars library for calculation of the collective
variables and the resulting forces. The default is <I>no</I>, i.e. to use the
current local coordinates that are wrapped back into the simulation cell
at each re-neighboring. Setting this to <I>yes</I> will use the image flags
to reconstruct the absolute atom positions.
</P>
<P>The <I>tstat</I> keyword can be either NULL or the label of a thermostating
fix that thermostats all atoms in the fix colvars group. This will be
used to provide the colvars module with the current thermostat target

11
doc/fix_colvars.txt
View File

@ -19,12 +19,14 @@ keyword = {input} or {output} or {seed} or {tstat} :l
{input} arg = colvars.state file name or prefix or NULL (default: NULL)
{output} arg = output filename prefix (default: out)
{seed} arg = seed for random number generator (default: 1966)
{unwrap} arg = {yes} or {no}
use unwrapped coordinates in collective variables (default: no)
{tstat} arg = fix id of a thermostat or NULL (default: NULL) :pre
:ule
[Examples:]
fix colvars peptide peptide.colvars.inp seed 2122 input peptide.colvars.state output peptide
fix colvars peptide peptide.colvars.inp seed 2122 input peptide.colvars.state output peptide unwrap yes
fix colvars all colvars.inp :pre
[Description:]
@ -66,6 +68,13 @@ a word like "state" or "traj".
The {seed} keyword contains the seed for the random number generator
that will be used in the colvars module.
The {unwrap} keyword controls whether wrapped or unwrapped coordinates
are passed to the colvars library for calculation of the collective
variables and the resulting forces. The default is {no}, i.e. to use the
current local coordinates that are wrapped back into the simulation cell
at each re-neighboring. Setting this to {yes} will use the image flags
to reconstruct the absolute atom positions.
The {tstat} keyword can be either NULL or the label of a thermostating
fix that thermostats all atoms in the fix colvars group. This will be
used to provide the colvars module with the current thermostat target