VMD-L Mailing List
From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Mar 08 2006 - 10:02:25 CST
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Hi,
you can actually use NAMDGui for this; it is a closely related plugin
designed to set up config files for (and run) general purpose namd jobs.
Running namdgui -nogui allows you to wrap it in a script; for example,
set sel [atomselect top all]
for {set i 0} {$i < [molinfo top get numframes]} {incr i 10} {
$sel frame $i
$sel writepdb namd-temp.pdb
namdgui -nogui -psf psffile -pdb namd-temp.pdb -o minimize-$i -min 1000
-run 0 -par parfile
}
$sel delete
should do something like what you want (with some of the parameters
tuned for how often you want snapshots and how long you want the
minimization to be). Is this what you're looking for? Please let me know
if you have any problems.
Best,
Peter
John Stone wrote:
>Hi,
> You should be able to invoke the NAMD Energy plugin in VMD 1.8.4 from
>the command line or from a script, with the same essential parameters that
>you would have specified in the graphical interface. See the NAMD Energy
>plugin web page:
> http://www.ks.uiuc.edu/Research/vmd/plugins/namdenergy/
>
>Let us know if you need more help with that.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
>On Wed, Mar 08, 2006 at 03:41:37PM +0100, L. Michel Espinoza-Fonseca wrote:
>
>
>>Dear all,
>>
>>I was wondering if somebody has designed a script (similar to
>>namd_energy) to minimize an ensemble of structures from a trajectory.
>>
>>Thanks!
>>
>>Michel
>>
>>
>
>
>
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