[gmx-users] regarding gen_seed

[Sathish Kumar]

dear João

Thank you very much for your help.


regards
Sathish

On Wed, Sep 21, 2016 at 7:13 AM, João Henriques <
joao.henriques.32353 at gmail.com> wrote:

> 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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-- 
regards
M.SathishKumar