[gmx-users] Regarding using random seed

[Tsjerk Wassenaar]

Right!

T.
On Mar 9, 2016 12:24 PM, "neha chaudhary" <nehachaudhary769 at gmail.com>
wrote:

> Hi,
>
> So all I have to do is to extract different configurations from my already
> performed MD simulation. Then I have to prepare a new system using that
> configuration with the following parameters and rerun the simulations:
>
> continuation = no
> gen_vel = yes
> gen-seed = -1
>
> Right?
>
>
> 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 4:06 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> wrote:
>
> > 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.
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