[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...;)


> 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


More information about the gromacs.org_gmx-users mailing list