There are example scripts for using this package with LAMMPS in -examples/USER/colvars. +
This documentation describes only the fix colvars command itself and +LAMMPS specific parts of the code. The full documentation of the +colvars library is available as this supplementary PDF document
-The implementation of the portable collective variable library is also -documented in (Henin) +
A detailed discussion of the implementation of the portable collective +variable library is in (Fiorin). Additional information can +be found in (Henin). +
+There are some example scripts for using this package with LAMMPS in the +examples/USER/colvars directory.
The only mandatory argument to the fix is the filename to the colvars -input file that contains all input that is independent from the MD +input file that contains the input that is independent from the MD program in which the colvars library has been integrated.
The group-ID entry is ignored. The collective variable module will -always apply to the entire system, i.e. use the group all. +always apply to the entire system and there can only be one instance +of the colvars fix at a time. The colvars fix will only communicate +the minimum information necessary and the colvars library supports +multiple, completely independent collective variables, so there is +no restriction to functionaliry by limiting the number of colvars fixes.
The input keyword allows to specify a state file that would contain -the information required in order to continue a calculation, e.g. -from a restart. Setting it to NULL will start a new colvars run. +the restart information required in order to continue a calculation from +a prerecorded state. Fix colvars records it state in binary restart +files, so when using the read_restart command, +this is usually not needed.
The output keyword allows to specify the output prefix. All output files generated will use this prefix followed by the ".colvars." and @@ -90,8 +98,10 @@ temperature.
Restart, fix_modify, output, run start/stop, minimize info:
-No information about this fix is written to binary restart -files. +
This fix writes the current status of the colvars module into +binary restart files. This is in addition to the text +mode status file that is written by the colvars module itself and the +kind of information in both files is identical.
The fix_modify energy option is supported by this fix to add the energy change from the biasing force added by the fix @@ -109,10 +119,10 @@ calculated by this fix is "extensive". LAMMPS was built with that package. See the Making LAMMPS section for more info.
-There can only be one colvars fix active at a time. Since the -colvars module itself can handle an arbitrary number of collective -variables and always applies to the entire system, this is not -really a deficit in practice. +
There can only be one colvars fix active at a time. Since the interface +communicates only the minimum amount of information and colvars module +itself can handle an arbitrary number of collective variables, this is +not a limitation of functionality.
Related commands:
@@ -125,9 +135,13 @@ and tstat = NULL.(Fiorin) Fiorin , Klein, Henin, Mol. Phys., DOI:10.1080/00268976.2013.813594 +
-(Henin) Hénin, Fiorin, Chipot, Klein, J. Chem. Theory Comput., 6, +
(Henin) Henin, Fiorin, Chipot, Klein, J. Chem. Theory Comput., 6, 35-47 (2010)