VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 13 2017 - 11:51:55 CDT

Hi,
  The NAMD Energy plugin is largely just a simple graphical interface
that generates the necessary NAMD config file to perform the requested
calculations by re-running NAMD on a trajectory file. The plugin itself
mostly just communicates with NAMD which does all of the work since as
you point out, it would be impossible to separate different force/energy
contributions ex post facto, so these are calculations that have to be
done inside of NAMD itself.

Best,
  John Stone

On Tue, Sep 12, 2017 at 02:37:30PM +0000, Michael LeVine wrote:
> Hi all,
> I am calculating the non-bonded interaction energy between an ion and its
> coordinating residues over the course of a simulation using the NAMD
> Energy Plug-in. While NAMD Energy has the option to use PME in the
> calculation, which we used during our simulations, it is not clear to me
> how the plug-in is calculating the portion of the long-range electrostatic
> interaction. It is my understanding that once using PME, the long-range
> electrostatic terms can't be trivially decomposed. Is the plug-in only
> outputting the short-range interaction terms?
> Thanks,
> Michael
> --
> Michael V. LeVine, PhD
> Institute Fellow, Institute for Computational Medicine
> Instructor in Physiology and Biophysics
>
> Instructor in Computational Biomedicine
> Department of Physiology and Biophysics, Weill Cornell Medicine 

-- 
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/