[gmx-users] calculate average and maximum non-bonded energy between energy groups

Justin Lemkul jalemkul at vt.edu
Wed Aug 26 12:00:30 CEST 2015

On 8/26/15 5:55 AM, Tushar Ranjan Moharana wrote:
> Hi Vitaly,
> Thanks for your suggestion. I have 30 energy groups. I faced following
> problems while using gmx energy.
> 1) With gmx energy there are more than 3000 options to choose from. All the
> options are not visible in terminal because of large number. There for I
> cann't proceed further.

Use a bigger terminal, or at least one that allows scrolling...

> 2) Output of gmx energy is a .xvg file with X axis as time and Y axis as
> energy between 2 groups. To get the data the way I need (X axis energy
> group and Y axis total energy with all other groups) I have to again
> process them with some other tool.

Right, see gmx analyze.

> Out put of gmx energy has time in X axis and energy in Y axis. The maximum
> value of which I referred to as  maximum interaction energy. (This mayn't
> be the exact definition).

I would agree with Vitaly that this is really not a useful quantity.  It is 
force field-specific and not necessarily anything to do with thermodynamics or 
free energy.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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