[gmx-users] Doubts regarding gen-seed, ld-seed and .cpt file.

[Mark Abraham]

Hi,

On Thu, 24 Jan 2019 at 10:22 Maity, Sayan <s.maity at jacobs-university.de>
wrote:

> Hi Mark,
>
>
> So basically, in order to reproduce the simulation, I need to fix both
> seed numbers in the .mdp file right ...??
>

No, I said the seeds were fixed *after* you run grompp. That is, the .tpr
is in principle reproducible, caveat the usual things
http://manual.gromacs.org/current/user-guide/managing-simulations.html#reproducibility.
That's because the velocities have already been generated (if requested
with gen-vel, and so gen-seed is then irrelevant), and ld-seed has a
definite value (as you can see with gmx dump, or in the subsequent mdrun
log file).


> However, I can find the ld-seed number from the .log file but I didn't
> find any gen-seed number. So in which file I could get the gen-seed number
> if the previous simulation was done considering gen-seed=-1....??
>

grompp reported it in its terminal output. But you never need it again.

Another question is that,
>
>
> Is ld-seed number is also taking random velocity from Boltzmann
> distribution...?


No, some algorithm that you haven't mentioned may be using numbers from a
random number generator that was seeded with that value :-)

So, if gen-seeds are same but ld-seeds are different, can I call it as a
> different simulation for the same starting structure...?
>

The trajectories will diverge soon.

Mark


> Thanks.
>
> Sayan
>
>
> --
>
> Sayan Maity
>
> Workgroup of Prof. Dr. Ulrich Kleinekathöfer
>
> Ph.D. Student/Research Associate
>
> Jacobs University Bremen gGmbH, Germany
>
>
> https://www.jacobs-university.de/directory/maity
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mark
> Abraham <mark.j.abraham at gmail.com>
> Sent: Thursday, January 24, 2019 9:20:41 AM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Doubts regarding gen-seed, ld-seed and .cpt file.
>
> Hi,
>
> Both these seeds are fixed after you run grompp. That has no relationship
> to whether velocities are present from any input file. There is also no
> difference between NVT and NPT.
>
> I assume that your non-reproducible cases are each running grompp with one
> of these seed values set to -1, in which case grompp can picks a different
> value each time you run it. Otherwise, please show your command lines :-)
>
> Mark
>
> On Wed, 23 Jan 2019 at 16:55 Maity, Sayan <s.maity at jacobs-university.de>
> wrote:
>
> > Dear All,
> >
> >
> > I have a doubt regarding the ld-seed no and .cpt file. If you repeat a
> > simulation with the same .cpt file but different ld-seed no, my guess I
> > should get the same trajectory running in the serial node (1node+1core ),
> > as because of all the velocities are stored in the .cpt file. I did this
> > test but the trajectories are different unless I fixed the ld-seed no.
> So,
> > my point is what is the significance of using .cpt file when you are
> doing
> > a production run from an equilibration as velocity is already there in
> the
> > .gro file....?? and why ld-seed no is controlling the dynamics not the
> > gen-seed....? I checked that for nvt I need to specify both gen-seed and
> > ld-seed in order to reproduce the trajectory, but from npt, I only need
> the
> > ld-seed to reproduce the trajectory. Could you please clarify my
> doubts...??
> >
> >
> > Thanks.
> >
> >
> > Regards,
> >
> > Sayan
> >
> > --
> >
> > Sayan Maity
> >
> > Workgroup of Prof. Dr. Ulrich Kleinekathöfer
> >
> > Ph.D. Student/Research Associate
> >
> > Jacobs University Bremen gGmbH, Germany
> >
> >
> > https://www.jacobs-university.de/directory/maity
> > --
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> >
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