[gmx-users] Regarding using random seed

[Tsjerk Wassenaar]

Hi Neha,

Set

continuation = no
gen_vel = yes

(check http://manual.gromacs.org/online/mdp_opt.html#vel)

Best,

Tsjerk


On Wed, Mar 9, 2016 at 11:16 AM, neha chaudhary <nehachaudhary769 at gmail.com>
wrote:

> 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,
> > > --
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> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
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-- 
Tsjerk A. Wassenaar, Ph.D.