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 @@
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)
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.inpDescription: @@ -74,6 +76,13 @@ 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 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