Hi
That should work.
For the future, you can just set ig = -1, and that will create a new
seed from the system's clock, so it should be different every time.
Adrian
On 8/17/26 5:59 AM, ABDELATIF MESSAOUDI via AMBER wrote:
> [External Email]
>
> Dear Users
>
> I would appreciate your advice regarding a reviewer comment on our
> molecular dynamics study.
>
> The reviewer requested the following:
>
> “Authors perform and report replicate molecular dynamics simulations for
> the four protein-ligand complexes (6XES-P15, 6XES-P10, 5CA1-P8, 5CA1-P15)
> to validate the reliability and reproducibility of the simulation results.”
>
> I have already performed the MD simulations for these four protein–ligand
> complexes. To address the reviewer’s request, I have tried to run three
> independent MD simulations for each system.
>
> For this purpose, I used the same simulation protocol but changed the
> random seed (ig) in the heating input file for each replicate. For example:
>
> # heat1.in
> heat
> &cntrl
> imin=0, nstlim=10000,
> dt=0.002, ntc=2, ntf=2, nrespa=1,
> ntpr=500, ntwx=500,
> ntt=3, gamma_ln=2, tempi=100, temp0=298, tautp=2.0,
> iwrap=1, ioutfm=1,
> ntb=1,
> irest=0, ntx=1,
> nmropt=0,
> ig=11111,
> /
>
> For the three replicas, I changed the random seed as follows:
>
> - Replica 1: ig=11111
> - Replica 2: ig=22222
> - Replica 3: ig=33333
>
> I kept the rest of the simulation parameters identical.
>
> Could you please let me know whether this approach is scientifically and
> technically appropriate for generating independent replicate simulations in
> AMBER? In particular, I would like to make sure that simply changing the ig
> value is sufficient to consider the simulations as independent replicas, or
> whether I should modify other aspects of the setup.
>
> I can also send you my complete AMBER input files and scripts for the
> heating, equilibration, and production stages if that would help you
> evaluate whether the setup is correct.
>
> Thank you very much in advance for your help and advice.
>
> Best regards,
>
> Abdelatif Messaoudi
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr. Adrian E. Roitberg
Frank E. Harris Professor
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 17 2026 - 08:30:02 PDT
