[gmx-users] Re: distance restraint

Justin Lemkul 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.

> 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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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