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 <sathishk...@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 -- 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.