diff --git a/doc/fix_adapt_fep.html b/doc/fix_adapt_fep.html index ebd1434bf8..ffc2d9a8d1 100644 --- a/doc/fix_adapt_fep.html +++ b/doc/fix_adapt_fep.html @@ -64,13 +64,16 @@ fix 1 all adapt/fep 10 atom diameter 1 v_size
Description:
Change or adapt one or more specific simulation attributes or settings -over time as a simulation runs. +over time as a simulation runs.
-This is a version of the fix_adapt with two -differences, +
This is an enhanced version of the fix_adapt command +with two differences,
-This version is suited for free energy calculations using compute_ti or compute_fep. @@ -98,10 +101,10 @@ the parameters themselves are actually altered; make sure you use the initial values after the run.
If the after keyword is set to yes, then the parameters are -changed one timestep after the multiple of N. In this manner, if a -fix such as "fix ave/time" is used to calculate averages at every N +changed one timestep after the multiple of N. In this manner, if a fix +such as "fix ave/time" is used to calculate averages at every N timesteps, all the contributions to the average will be obtained with -the same values of the parameters. +the same values of the parameters.
Related commands:
-compute fep -fix_adapt -compute ti +
compute fep, fix_adapt, compute +ti
Default:
diff --git a/doc/fix_adapt_fep.txt b/doc/fix_adapt_fep.txt index 7921ea76be..db795ef853 100644 --- a/doc/fix_adapt_fep.txt +++ b/doc/fix_adapt_fep.txt @@ -52,15 +52,16 @@ fix 1 all adapt/fep 10 atom diameter 1 v_size :pre [Description:] Change or adapt one or more specific simulation attributes or settings -over time as a simulation runs. +over time as a simulation runs. -This is a version of the "fix_adapt"_fix_adapt.html with two -differences, +This is an enhanced version of the "fix_adapt"_fix_adapt.html command +with two differences, -It is possible to modify the charges of chosen atom types only, \ -instead of scaling all the charges in the system. -There is a new option {after} for better compatibility with "fix\ -ave/time". :ul +It is possible to modify the charges of chosen atom types only, +instead of scaling all the charges in the system. :ulb,l + +There is a new option {after} for better compatibility with "fix +ave/time". :l,ule This version is suited for free energy calculations using "compute_ti"_compute_ti.html or "compute_fep"_compute_fep.html. @@ -88,10 +89,10 @@ the parameters themselves are actually altered; make sure you use the initial values after the run. If the {after} keyword is set to {yes}, then the parameters are -changed one timestep after the multiple of N. In this manner, if a -fix such as "fix ave/time" is used to calculate averages at every N +changed one timestep after the multiple of N. In this manner, if a fix +such as "fix ave/time" is used to calculate averages at every N timesteps, all the contributions to the average will be obtained with -the same values of the parameters. +the same values of the parameters. :line @@ -247,9 +248,8 @@ This fix is not invoked during "energy minimization"_minimize.html. [Related commands:] -"compute fep"_compute_fep.html -"fix_adapt"_fix_adapt.html -"compute ti"_compute_ti.html +"compute fep"_compute_fep.html, "fix_adapt"_fix_adapt.html, "compute +ti"_compute_ti.html [Default:]