[gmx-users] confusion on energy for a system of protein sovated in water

Justin Lemkul jalemkul at vt.edu
Tue Feb 23 02:36:15 CET 2016

On 2/22/16 8:33 PM, Ming Tang wrote:
> Dear lists,
> After pulling a protein in water and performing mdrun -rerun, I found that
> G96Bond, G96Angle, COM-Pull-En and Potential energy extracted from the
> original system using g_energy -f ener.edr , and from the -rerun system using
> g_energy -f rerun.edr have different values.
> Firstly, are those values the energy of the system?

Bond, angle, energy of the spring, and potential energy of the system.

> Secondly, why are they different?

Why did you do a rerun and what did you change about the .tpr file in doing so?



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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