From: sajad falsafi (sajad.falsafi_at_yahoo.com)
Date: Wed Nov 09 2011 - 23:16:18 CST
--- On Thu, 11/10/11, Richard Wood <rwoodphd_at_yahoo.com> wrote:
> From: Richard Wood <rwoodphd_at_yahoo.com>
> Subject: namd-l: two NAMD questions
> To: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>
> Date: Thursday, November 10, 2011, 8:01 AM
> Hi all,
>
> I have two questions about NAMD. I've looked
> online and in tutorials and have even gone through the
> archive and can't find answers to my problems.
> The first is probably simpler than the second.
>
> Is it possible to write a script to submit more than one
> NAMD input file so that one will run after the first one
> finishes, and if so, how do I do that?
> I'm running NAMD under Windows, so I'd do it from
> the command prompt.
yes, you can write script for it.
>
> Secondly, does anybody have a script that I could borrow to
> run a simulated annealing calculation? I have a whole
> bunch of these that I want to
> run which is why I'd like to run them in "batch
> mode".
you can write something like this:
reassignFreq 100
reassignTemp 0
minimize 1000
for { set TEMP 0 } { $TEMP < 310 } { incr TEMP 10 } {
run 100
reassignTemp $TEMP
}
run 1000
for { set TEMP 300 } { $TEMP >= 0 } { incr TEMP -10 } {
reassignTemp $TEMP
run 100
}
>
> TIA,
> Richard
Best of luck,
Sajad Falsafi
Dept. of Genetics, Shahid Chamran University of Ahvaz
Toxicology Research Center, Jondi-Shapour University of Medical Sciences
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