thanks a bunch for the input. On Thu, Sep 10, 2009 at 9:38 AM, Justin A. Lemkul <jalem...@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: > > 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.a...@gmail.com <mailto: >> kgp.a...@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 >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > ======================================== > > 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 > > ======================================== > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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