[gmx-users] initial velocities analysis
Justin A. Lemkul
jalemkul at vt.edu
Wed Aug 25 21:36:45 CEST 2010
Anna Marabotti wrote:
> Dear gmx-users,
> sorry for my trivial questions, but I didn't find an answer searching in
> the Gromacs web site.
> I want to generate different trajectories on my system, and I used an
> .mdp file in which I set gen_seed = -1 together with gen_vel = yes and
> continuation = no to do this quickly. If I understand well, every time I
> launch my simulation, Gromacs will generate a different initial
> velocity. My questions are:
> - if I want to launch 5 different simulation, fixing gen_seed = -1 in my
> .mdp file I should obtain different results without doing every time
> grompp+mdrun. After the first grompp+mdrun, I have the .tpr file that
> includes already the information to generate random velocities,
> therefore for the second, third...etc. run I simply have to launch mdrun
> using the same .tpr file, right?
I believe the velocities are generated by grompp, not mdrun, and thus are
already set in the .tpr file. Whether or not you get a binary reproducible
trajectory is another matter, but I would not consider these "independent"
> - is there a way to check for the velocities or for the random seed
> used? I had a look at the .log file but I didn't find the information.
> g_traj generated a very big file, and presently I have some problems to
> analyze it. How can I see initial velocities?
Use gmxdump on the .tpr file and read what the velocities are. You can compare
two .tpr files to see if they are different with gmxcheck -s1 -s2.
> Many thanks and best regards
> Anna Marabotti, Ph.D.
> Laboratory of Bioinformatics and Computational Biology
> Institute of Food Science, CNR
> Via Roma, 64
> 83100 Avellino (Italy)
> Phone: +39 0825 299651
> Fax: +39 0825 781585
> Email: anna.marabotti at isa.cnr.it <mailto:anna.marabotti at isa.cnr.it>
> Skype account: annam1972
> Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
> "If you think you are too small to make a difference, try sleeping with
> a mosquito"
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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