[gmx-users] inconsistent energy drops

Justin Lemkul jalemkul at vt.edu
Wed Jul 31 22:12:57 CEST 2013

On 7/31/13 3:38 PM, Brad Van Oosten wrote:
> Hello,
> I am performing a MD simulation on a small molecule in a bilayer.  The
> simulation seems to run smoothly but when i graph the energy i see large
> changes in energy randomly throughout the run(see graph).
> <http://gromacs.5086.x6.nabble.com/file/n5010260/potential_12cc50.png>
> I have looked at each energy term individually and it is the coulomb (SR)
> which has these large jumps while the rest seem to be normal.
> Can anyone suggest what might be going on here? (i can add the mdp file if
> needed)

Does visualization of the trajectory indicate anything?  The two downward spikes 
towards the beginning of the run (within 10 ns) should be easy to identify since 
they stand out very clearly.  A binding event or structural change of some sort? 
  Reorientation of lipid headgroups, because of such large dipoles, could play a 
role here, especially if your small molecule is reacting accordingly.



Justin A. Lemkul, Ph.D.
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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