Re: [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.32...@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 
> 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:42Protein 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 
> > 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
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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regards
M.SathishKumar
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Re: [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 
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:42Protein 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 
> 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
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [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:42Protein 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 
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
-- 
Gromacs Users mailing list

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Re: [gmx-users] regarding gen_seed

[Justin Lemkul]

On 9/20/16 6:48 AM, Sathish Kumar wrote:

Dear gromacs-users,

 I want to run simulation of system of
peptide with carbon nanotube. And I want to run multiple simulations for
the same initial structure using different random initial velocities. For
that which values I have to use in the case of gen_seed=-1. Instead of -1
which values Can I use for gen_seed? is there any other way to assign
different random velocities.



gen_seed takes any integer as a value.  Using -1 is typically fine for just 
about everything, unless you need a record of exactly which seed was used (but 
that's printed to mdout.mdp and md.log, anyway).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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