Re: Re: vmd-l: NAMD energy calculation

From: Ramin Ekhteiari (
Date: Tue Jul 01 2014 - 12:07:47 CDT

Dear Brittany, Would you please let me know more about your script. I would like to do the same. Thanks Ramin. 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. Brittany ________________________________________ 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 Hi,   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. Cheers,   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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