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

[Maity, Sayan]

Hi Mark,


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


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....??



Another question is that,


Is ld-seed number is also taking random velocity from Boltzmann distribution...? So, if gen-seeds are same but ld-seeds are different, can I call it as a different simulation for the same starting structure...?


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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