From: Morgan, Brittany (Brittany.Morgan_at_umassmed.edu)
Date: Tue Jul 01 2014 - 09:26:44 CDT
I perform residue/residue energy calculations by creating batch scripts to perform each pair as an individual calculation so I can run them in parallel. It isn't fast, but it is doable.
From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of John Stone [johns_at_ks.uiuc.edu]
Sent: Monday, June 30, 2014 11:59 PM
To: Ramin Ekhteiari; David Hardy; Kirby Vandivort
Cc: VMD Mailing List; Namd Mailing List
Subject: namd-l: Re: vmd-l: NAMD energy calculation
I don't think there's any way to make the existing NAMDEnergy plugin
run much faster, as it basically just writes a configuration file
and starts NAMD to do the calculations. The only suggestion I have
is that since it runs NAMD, you might be able to do your specific
calculations in some more efficient way than the NAMDEnergy plugin
knows how to do, but you would have to become an expert at doing
these energy evaluations using the NAMD input scripts, etc. There may
also be other tools that can do these calculations more rapidly than
NAMD does, since this is a somewhat unusual use case for NAMD, and
there may be specific tools that are designed to be much faster
for this precise type of calculation. Sometime in the next year we
hope to have an alternative to NAMDEnergy that is much faster for
some of the cases that NAMDEnergy doesn't handle well, but I can't
say for sure if that will address your particular issue or not.
On Wed, Jun 25, 2014 at 09:45:33AM -0700, Ramin Ekhteiari wrote:
> Hi dears,
> I 'm trying to calculate the non-binding energies of hundreds of amino
> acid residues during MD simulation by using NAMD energy plugin. I preform
> this calculation one by one for each amino acid residue (e.g. resid 24
> with resid 36), so it takes a lot times, Is there any way for calculating
> these at one run and creating output of pair of residues interactions.
> Would be grateful for any advice.
-- NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/
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