[gmx-users] regarding gen_seed

[João Henriques]

Dear Sathish,

http://manual.gromacs.org/online/mdp_opt.html#vel

When using "gen_seed = -1", grompp will assign a seed based on the PID of
that process. Every time you re-run grompp it will assign a different seed,
because the respective PID for that grompp execution is also different.
This more or less guarantees that the seeds will always be sort of random.

So, yes, if you want to have different initial velocities, use gen_seed =
-1 at will.

Best regards,
João



On Wed, Sep 21, 2016 at 3:22 PM, Sathish Kumar <sathishk238 at gmail.com>
wrote:

> Dear gromacs-users
>
>                                         I created tpr file for nvt
> equilibration using mdp file in that mentioned gen_seed=-1.
>
> after creating tpr file, it shows as follows
>
> Generated 5050 of the 5050 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 5050 of the 5050 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'Other'
> turning H bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'Protein'
> turning H bonds into constraints...
> Excluding 2 bonded neighbours molecule type 'SOL'
> turning H bonds into constraints...
> Setting gen_seed to 49304
> Velocities were taken from a Maxwell distribution at 300 K
> Analysing residue names:
> There are:  1440      Other residues
> There are:    42    Protein residues
> There are: 35204      Water residues
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> into groups...
> Analysing Protein...
> Number of degrees of freedom in T-Coupling group Other is 4319.94
> Number of degrees of freedom in T-Coupling group Protein is 1028.99
> Number of degrees of freedom in T-Coupling group SOL is 211221.08
> Largest charge group radii for Van der Waals: 0.040, 0.040 nm
> Largest charge group radii for Coulomb:       0.079, 0.079 nm
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 80x80x48, spacing 0.150 0.150 0.157
> Estimate for the relative computational load of the PME mesh part: 0.23
>
>
> above you can see that setting gen_seed = 49304
>
> If I am creating again tpr file for nvt using same file then gen_seed =
> 50202 is coming. And I checked the velocities of atoms in two tpr files,
> those are different. Can I use these tpr files which created in this way to
> do multiple simulations on the same initial structure with different
> initial velocities.
>
> And I have seen the mdout.mdp file which created during generation of
> npt.tpr, in that gen_seed = 173529. In npt.mdp file, I have not used
> gen_seed option. Can anyone please explain me why it is showing like this?
>
> Thanks
> Sathish
>
>
>
>
> On Tue, Sep 20, 2016 at 11:52 PM, Sathish Kumar <sathishk238 at gmail.com>
> wrote:
>
> > Dear Justin
> >
> > Thank you very much for your reply. So, Is that  I can use gen_seed=5,
> > gen_seed=10 to assign different initial velocities for the same initial
> > structure?
> >
> >
> >
> > Thanks
> > Sathish
> >
>
>
>
> --
> regards
> M.SathishKumar
> --
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