[gmx-users] initial velocities analysis

Anna Marabotti anna.marabotti at isa.cnr.it
Wed Aug 25 15:48:03 CEST 2010

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?
- 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?
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
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
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