RE: Re: vmd-l: NAMD energy calculation

From: Morgan, Brittany (
Date: Wed Jul 02 2014 - 11:58:22 CDT

Hi Ramin,

In whatever scripting language you prefer, for each residue/residue pair:

1. Create a TCL script to run NAMDenergy for that residue pair.

2. Create a submission script for your queuing system that calls the TCL script.

3. Add your submission command (i.e. qsub NAME1) to a batch file so you don't have to submit each one individually.

It is typical to have a cap on the number of jobs that can be in the queue for a single user, so I suggest using multiple batch files to submit the jobs.

Good luck,


From: Ramin Ekhteiari []
Sent: Tuesday, July 01, 2014 1:07 PM
To: Morgan, Brittany; John Stone; David Hardy; Kirby Vandivort
Cc: VMD Mailing List; Namd Mailing List
Subject: Re: namd-l: Re: vmd-l: NAMD energy calculation

Dear Brittany,

Would you please let me know more about your script.
I would like to do the same.


On Tuesday, July 1, 2014 5:26 PM, "Morgan, Brittany" <> wrote:

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:<> [<>] on behalf of John Stone [<>]
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.

  John Stone<>

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.
> Cheers,
> Ramin

NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801           Phone: 217-244-3349

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