[gmx-users] Positive Potential Energy.

Justin Lemkul jalemkul at vt.edu
Thu Aug 28 20:21:00 CEST 2014

On 8/28/14, 2:04 PM, Dan Sponseller wrote:
> Hello everyone.
> I am still fairly new to gromcs but I have researched this well.
> I am getting a positive potential energy (my bond energy is always positive) no matter how long I run my simulation. I also get this when doing minimizations. Even just one molecule set at know minimum conformation.

Bond energy can only ever be zero (all bonds at exactly equilibrium values) or 
positive (not equilibrium values).

> I am running in vacuo with no pbc. I have read on the mail list that in vacuo can produce this? This doesn’t make sense as the molecule should fly apart with always positive PE.
> I have tried gromos ff and opsla ff. Both do this. A colleague of mine also  gets this with his simulations although he reports negative potential when solvated.

Negative potentials in condensed phase systems occur because of the massive 
amount of favorable nonbonded interactions, particularly hydrogen bonding 
between waters and with solute.

> Any help would be appreciated or any explanation on how to interpret gromacs output on this.
> I would question gromacs’ abilities if it cannot give a reasonable potential energy for a simple system.

What is the system?  Positive energy is indeed reasonable in vacuo.



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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