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.
Paula
Here is the graph of energy of distance restraint
<http://gromacs.5086.n6.nabble.com/file/n5001409/Screenshot-1.png>
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
--
========================================
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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