On 7/2/12 4:51 PM, Laura Kingsley wrote:
Basically what I'm doing is pulling a ligand out of a protein towards a dummy
atom, which has a mass of 1 and no charge. I've attached the a portion .mdp
files for both the smd portion and the umbrella sampling. I know that the ligand
gets very close possibly crashing into the dummy atom. So from what you're
saying, I'm thinking this might be the source of the problem.
Sounds like it to me.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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