[gmx-users] regarding gen_seed

[Sathish Kumar]

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