From 3dadc962c02b028b86e45665d4121cfd689c2534 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Tue, 23 Apr 2013 19:04:04 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9786
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 doc/fix_colvars.html | 11 ++++++++++-
 doc/fix_colvars.txt  | 11 ++++++++++-
 2 files changed, 20 insertions(+), 2 deletions(-)

diff --git a/doc/fix_colvars.html b/doc/fix_colvars.html
index 6607fc976b..001aa8c6aa 100644
--- a/doc/fix_colvars.html
+++ b/doc/fix_colvars.html
@@ -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
diff --git a/doc/fix_colvars.txt b/doc/fix_colvars.txt
index 432d57161e..92a439c11c 100644
--- a/doc/fix_colvars.txt
+++ b/doc/fix_colvars.txt
@@ -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