[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
> ____________________________________________________
> 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
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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