diff --git a/doc/fix_colvars.html b/doc/fix_colvars.html index 001aa8c6aa..c622a6ff4f 100644 --- a/doc/fix_colvars.html +++ b/doc/fix_colvars.html @@ -27,15 +27,15 @@ 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) + use unwrapped coordinates in collective variables (default: yes) 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 unwrap yes
-fix colvars all colvars.inp 
+
fix mtd all colvars peptide.colvars.inp seed 2122 input peptide.colvars.state output peptide
+fix abf all colvars colvars.inp tstat 1 
 

Description:

@@ -78,10 +78,10 @@ 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. +variables and the resulting forces. The default is yes, i.e. to use +the image flags to reconstruct the absolute atom positions. +Setting this to no will use the current local coordinates that are +wrapped back into the simulation cell at each re-neighboring instead.

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 @@ -120,8 +120,8 @@ really a deficit in practice.

Default:

-

The default options are input = NULL, output = out, seed = 1966, and -tstat = NULL. +

The default options are input = NULL, output = out, seed = 1966, unwrap yes, +and tstat = NULL.


diff --git a/doc/fix_colvars.txt b/doc/fix_colvars.txt index 92a439c11c..caf04c14a9 100644 --- a/doc/fix_colvars.txt +++ b/doc/fix_colvars.txt @@ -20,14 +20,14 @@ keyword = {input} or {output} or {seed} or {tstat} :l {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) + use unwrapped coordinates in collective variables (default: yes) {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 unwrap yes -fix colvars all colvars.inp :pre +fix mtd all colvars peptide.colvars.inp seed 2122 input peptide.colvars.state output peptide +fix abf all colvars colvars.inp tstat 1 :pre [Description:] @@ -70,10 +70,10 @@ 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. +variables and the resulting forces. The default is {yes}, i.e. to use +the image flags to reconstruct the absolute atom positions. +Setting this to {no} will use the current local coordinates that are +wrapped back into the simulation cell at each re-neighboring instead. 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 @@ -112,8 +112,8 @@ really a deficit in practice. [Default:] -The default options are input = NULL, output = out, seed = 1966, and -tstat = NULL. +The default options are input = NULL, output = out, seed = 1966, unwrap yes, +and tstat = NULL. :line diff --git a/doc/pair_coeff.html b/doc/pair_coeff.html index da6b3ea192..28e0cbf7e2 100644 --- a/doc/pair_coeff.html +++ b/doc/pair_coeff.html @@ -104,8 +104,8 @@ section of this page.
  • pair_style bop - BOP potential of Pettifor
  • pair_style born - Born-Mayer-Huggins potential
  • pair_style born/coul/long - Born-Mayer-Huggins with long-range Coulombics -
  • >pair_style born/coul/msm - Born-Mayer-Huggins with long-range MSM Coulombics -
  • pair_style born/coul/wolf - Born-Mayer-Huggins with Coulombics via Wolf potential +
  • pair_style born/coul/msm - Born-Mayer-Huggins with long-range MSM Coulombics +
  • pair_style born/coul/wolf - Born-Mayer-Huggins with Coulombics via Wolf potential
  • pair_style brownian - Brownian potential for Fast Lubrication Dynamics
  • pair_style brownian/poly - Brownian potential for Fast Lubrication Dynamics with polydispersity
  • pair_style buck - Buckingham potential diff --git a/doc/pair_coeff.txt b/doc/pair_coeff.txt index 438dee219d..2168345e20 100644 --- a/doc/pair_coeff.txt +++ b/doc/pair_coeff.txt @@ -102,7 +102,7 @@ section of "this page"_Section_commands.html#cmd_5. "pair_style born"_pair_born.html - Born-Mayer-Huggins potential "pair_style born/coul/long"_pair_born.html - Born-Mayer-Huggins with long-range Coulombics "pair_style born/coul/msm"_pair_born.html - Born-Mayer-Huggins with long-range MSM Coulombics -pair_style born/coul/wolf"_pair_born.html - Born-Mayer-Huggins with Coulombics via Wolf potential +"pair_style born/coul/wolf"_pair_born.html - Born-Mayer-Huggins with Coulombics via Wolf potential "pair_style brownian"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics "pair_style brownian/poly"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics with polydispersity "pair_style buck"_pair_buck.html - Buckingham potential diff --git a/doc/pair_style.html b/doc/pair_style.html index 6c8b05152c..aa3843f708 100644 --- a/doc/pair_style.html +++ b/doc/pair_style.html @@ -106,8 +106,8 @@ section of this page.
  • pair_style bop - BOP potential of Pettifor
  • pair_style born - Born-Mayer-Huggins potential
  • pair_style born/coul/long - Born-Mayer-Huggins with long-range Coulombics -
  • >pair_style born/coul/msm - Born-Mayer-Huggins with long-range MSM Coulombics -
  • pair_style born/coul/wolf - Born-Mayer-Huggins with Coulombics via Wolf potential +
  • pair_style born/coul/msm - Born-Mayer-Huggins with long-range MSM Coulombics +
  • pair_style born/coul/wolf - Born-Mayer-Huggins with Coulombics via Wolf potential
  • pair_style brownian - Brownian potential for Fast Lubrication Dynamics
  • pair_style brownian/poly - Brownian potential for Fast Lubrication Dynamics with polydispersity
  • pair_style buck - Buckingham potential diff --git a/doc/pair_style.txt b/doc/pair_style.txt index 1db783acb9..4372d04c6b 100644 --- a/doc/pair_style.txt +++ b/doc/pair_style.txt @@ -104,7 +104,7 @@ section of "this page"_Section_commands.html#cmd_5. "pair_style born"_pair_born.html - Born-Mayer-Huggins potential "pair_style born/coul/long"_pair_born.html - Born-Mayer-Huggins with long-range Coulombics "pair_style born/coul/msm"_pair_born.html - Born-Mayer-Huggins with long-range MSM Coulombics -pair_style born/coul/wolf"_pair_born.html - Born-Mayer-Huggins with Coulombics via Wolf potential +"pair_style born/coul/wolf"_pair_born.html - Born-Mayer-Huggins with Coulombics via Wolf potential "pair_style brownian"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics "pair_style brownian/poly"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics with polydispersity "pair_style buck"_pair_buck.html - Buckingham potential