[gmx-users] Re: bypassing pdb2gmx
kgp.amit at gmail.com
Fri Sep 11 10:34:06 CEST 2009
thanks a bunch for the input.
On Thu, Sep 10, 2009 at 9:38 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 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 :)
>> 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.
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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
> gmx-users mailing list gmx-users at gromacs.org
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