[gmx-users] Regarding using random seed

[neha chaudhary]

Thanks Tsjerk for replying,

I want to ask one more question that to start with new velocities, what
changes I have to make and in which .mdp file?

Best Regards,

*Neha*

Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Life Sciences,
Central University of Himachal Pradesh,





On Wed, Mar 9, 2016 at 3:37 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Neha,
>
> You can perform a simulation first, and then extract configurations, which
> you simulate with new starting velocities. Alternatively, you can generate
> a number of different starting structures using elastic-network modeling,
> like with the ElNemo server. Mind to first energy minimize the resulting,
> extrapolated structures, as they may be stretchedhere and there.
>
> Hope it helps,
>
> Tsjerk
>
> On Wed, Mar 9, 2016 at 10:54 AM, neha chaudhary <
> nehachaudhary769 at gmail.com>
> wrote:
>
> > Hello there,
> >
> >
> > Can anyone tell me how can I start my MD simulations with different
> > starting structure (random seed) for my protein-ligand complex. Can I
> start
> > with different sets of coordinates and velocities? If yes, how?
> >
> >
> > Thanks,
> >
> > *Neha*
> > Research Scholar,
> > Centre for Computational Biology and Bioinformatics,
> > School of Life Sciences,
> > Central University of Himachal Pradesh,
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>