[gmx-users] MD after equilibration phase

Mark Abraham Mark.Abraham at anu.edu.au
Fri Apr 6 16:56:24 CEST 2012

On 7/04/2012 12:37 AM, Justin A. Lemkul wrote:
> bipin singh wrote:
>> Thanks for your comments.
>> One more question.
>> Does Gromacs saves velocities in pdb files, when we use gen_vel=yes 
>> option in mdp and save the output(-c) of mdrun as pdb file instead of 
>> gro file.
> No.  Velocities are only saved in the .trr and/or .cpt files.  There 
> is no place for velocities in .pdb files.

It's conceivable that there are velocities in a mdrun -c 
finalstructure.gro file, but these would have to be only at low 
precision, and thus often useless.


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