[gmx-users] questions in Running MDS over docked poses
Justin A. Lemkul
jalemkul at vt.edu
Mon Nov 10 13:27:07 CET 2008
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 simulations.
> 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...;)
-Justin
> Waiting for suggestions.
>
> With Thanks,
> Vivek
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
More information about the gromacs.org_gmx-users
mailing list