[gmx-users] Regarding using random seed

[neha chaudhary]

Hello Sir,

Thanks for your help.

I need to clear one more doubt, if I am performing MD simulations with the
mentioned parameter set but using same initial structures then will it
affect the reproducibility of the results.
Actually, I have repeated MD simulations for my protein-ligand complex
three times but I have taken the same initial structure every time using
the same parameters while performing NVT simulations followed by NPT and MD
run (gen-vel = no in npt.mdp and md.mdp file). Is this procedure correct if
I want to testify the reliability of my results.

continuation = no
gen-vel = yes
gen-seed = -1


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 6:36 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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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