[gmx-users] Re: bypassing pdb2gmx

Justin A. Lemkul jalemkul at vt.edu
Thu Sep 10 18:38:42 CEST 2009

Amit Choubey wrote:
> hi everyone,
> I guess if i knew the exact format of .gro files i could write a small 
> code to copy data from pdb to gro . I cannot find this info anywhere. I 
> believe that it has co-ordinates and velocities but how are the 
> velocities choose (randomly?). I am also not sure abt the exact order.

The format is available as part of the online manual:


Although I don't know why you feel it necessary to write code that's already 
part of editconf.

Velocities are assigned randomly when grompp sees "gen_vel = yes" in the .mdp 
file, according to the gen_temp parameter.  I'd say keep life easy and use the 
functions Gromacs already provides you instead of writing code for converting 
coordinates and writing velocities :)


> Amit
> On Wed, Sep 9, 2009 at 5:29 PM, Amit Choubey <kgp.amit at gmail.com 
> <mailto:kgp.amit at gmail.com>> wrote:
>     hi everyone,
>     I have a pdb file of my system and i want it to be fed into the
>     GROMACS software. I have a new force field for the simulation and i
>     have made the .top file manually which includes the new library FF
>     files. I need to get a .gro file from the .pdb file that i have. So,
>     is there a way out to do this without incorporating pdb2gmx because
>     i dont use the standard FF and i dont really have all the other
>     datafiles for the new FF except for necessary bond and nonbonded infos.
>     Amit
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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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