[gmx-users] Regarding using random seed

[neha chaudhary]

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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