[gmx-users] questions in Running MDS over docked poses
viveksharma.iitb at gmail.com
Tue Nov 11 06:46:26 CET 2008
Thanks for your reply...
I am interested in looking for the stability of the docked pose, by applying
some temperature variation in the molecule.
If I am applying temperature variation then should I use pressure coupling
Can you suggest some tutorial for such attempts.....
2008/11/10 Justin A. Lemkul <jalemkul at vt.edu>
> vivek sharma wrote:
>> Hi There,
>> I am running MDS over the docked poses to check the stability of the
>> docked poses using gromacs.
>> I have few doubts about selecting parameters for the same, If anybody have
>> tried such thing earlier, please suggest me for the same.
>> Should I keep pressure coupling over the simulation ?
> Sure; life exists at NPT, so it is commonly used in routine protein
> For how long should I run the simulation for such purpose ?
> That's up to you :) You should run the simulations as long as you feel
> necessary to achieve stability. I know that's vague, but there really is no
> single correct answer to this question in the MD field. If there is, I'd
> love for someone to tell me, too...;)
> Waiting for suggestions.
>> With Thanks,
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> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
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