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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
View File

@ -26,13 +26,15 @@
<PRE> <I>input</I> arg = colvars.state file name or prefix or NULL (default: NULL) <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>output</I> arg = output filename prefix (default: out)
<I>seed</I> arg = seed for random number generator (default: 1966) <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) <I>tstat</I> arg = fix id of a thermostat or NULL (default: NULL)
</PRE> </PRE>
</UL> </UL>
<P><B>Examples:</B> <P><B>Examples:</B>
</P> </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 fix colvars all colvars.inp
</PRE> </PRE>
<P><B>Description:</B> <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 <P>The <I>seed</I> keyword contains the seed for the random number generator
that will be used in the colvars module. that will be used in the colvars module.
</P> </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 <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 fix that thermostats all atoms in the fix colvars group. This will be
used to provide the colvars module with the current thermostat target 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) {input} arg = colvars.state file name or prefix or NULL (default: NULL)
{output} arg = output filename prefix (default: out) {output} arg = output filename prefix (default: out)
{seed} arg = seed for random number generator (default: 1966) {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 {tstat} arg = fix id of a thermostat or NULL (default: NULL) :pre
:ule :ule
[Examples:] [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 fix colvars all colvars.inp :pre
[Description:] [Description:]
@ -66,6 +68,13 @@ a word like "state" or "traj".
The {seed} keyword contains the seed for the random number generator The {seed} keyword contains the seed for the random number generator
that will be used in the colvars module. 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 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 fix that thermostats all atoms in the fix colvars group. This will be
used to provide the colvars module with the current thermostat target used to provide the colvars module with the current thermostat target