Oguz, On Thu, Sep 30, 2010 at 4:52 PM, oguz gurbulak <[email protected]>wrote:
> Dear Dr. Roland Schulz, > > > > Thank you very much for your attention. I would like to have a copy of > patch that generates gromacs topology from psf file. And could you please > explain how to use this patch in detail ? Because I have no information on > Pär's scripts. > Do you have standard CHARMM or Amber FF? Than you don't need to convert the FF because it is already part of GROMACS. > > I think, In order to continue a NAMD simulation in Gromacs I should first > save the last coordinates (.coor file in namd ) as a pdb file and convert it > into gro file . But there are many ways to get a gro file > no you don't need to convert the coordinate file or get the last frame. > > > - using pdb2gmx ( but I should choose the force field in gromacs. This may > be a problem. ) By the way, I changed CHARMM force field and use Amber type > force field in NAMD. > Don't understand what you mean? Do you use CHARMM or Amber FF? If it is a standard molecule (e.g. protein), it will be much easier to just use pdb2gmx to generate the topology. > Could you share your ideas about this process ? What should I do ? > You would just do everything the same way as setting up a new simulation and use the last frame as starting structure. Make sure you use a structure which includes both coordinates and velocities. > Is there a way to get a tpr file from NAMD files? > No. Not automatically. You need to get all the input files (grompp.mdp, topol.top, conf.gro) and then run grompp to generate your tpr. Roland > > > > > Kind regards. > > > > > > Oguz GURBULAK Ph.D. Student > Ege University - Faculty of Science > Department of Physics > Branch of Atomic and Molecular Physics > > > > > > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
