Re: Implementation of TCL script in NAMD .conf file

From: Benjamin Bouvier (
Date: Mon Jul 07 2008 - 04:34:54 CDT


Take a look at the "checkpoint" and "revert" commands on page 17 of the
manual. Never used them myself, but they seem to apply to your problem.
You would then run a loop such as:

for {set i 0} {$i < $numcycles} {incr i} {
   run $nmdsteps
   minimize $nminsteps

Hope it helps,


Le Sat, 05 Jul 2008 07:18:25 +0200, sudipta sinha <>
a écrit:

> Hi All,
> I want to do a simulation in such a way that my system minimize
> 500
> steps at every saved frequency time steps. For example , suppose I am
> running a simulation of length 1 ns and I am saving the positions in
> a
> dcd files at a frequency 200. I want to minimize my system at each saved
> frequency but I don't want to save those informations during minimization
> and want only to save the final minimize configuration. Next step of
> simulation will run via the 0th minimize step configuration (i,e actual
> md
> step configuration). Is this scheme possible to implemented by TCL. If
> so,
> then how I can implement this scheme? I need your suggestions.
> Thanks in advance
> sudipta

Benjamin Bouvier

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