[gmx-users] initial velocities analysis

[Mark Abraham]

----- Original Message -----
From: Dmitri Dubov <ddubov at ngs.ru>
Date: Thursday, August 26, 2010 18:17
Subject: Re[2]: [gmx-users] initial velocities analysis
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

 
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> Hi, Justin.
 


 
> I'm also interested in this question. Could you make clear:
 


 
> > Anna Marabotti wrote:
 
...
 
>> - 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?
 
>>  
 
...
 


 
> In other words, when gen_seed is set to -1, there is a rigorous rule for seed calculation. How can I get the value of this seed? I need it to repeat exactly the same run, e.g., with more detailed outputs.




See manual 7.3.17, and inspect your mdrun .log file for the value grompp actually used. However, note http://www.gromacs.org/Documentation/Terminology/Reproducibility




Mark

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