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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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