[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:
http://manual.gromacs.org/current/online/gro.html
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 :)
-Justin
> 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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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