[gmx-users] Re: distance restraint
jalemkul at vt.edu
Fri Sep 28 18:40:30 CEST 2012
On 9/28/12 12:25 PM, pauladelgado wrote:
> Other thing is that i couldn't found a lot of literature about the conditions
> for vacuum simulations, can you help me with this please,
> Thanks a lot Justin
Searching Google Scholar for "protein vacuum simulations" (without quotes) turns
up 38000 results. Surely something in there will be of use. Scientific
database software will probably return even more pertinent results.
> Here is the graph of energy of distance restraint
This doesn't answer the question I posed before. Please measure distances
between the restrained atoms and compare with the restraints you're trying to
impose. The initial geometry may not be amenable to such restraints. The
magnitude of the energy suggests that your restraints are severely violated.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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