Dear Dr. Roland Schulz,
Thank you very much for your attention. I have Amber type ff that includes
bond, angle, dihedral and nonbounded interaction terms in Charmm file format.
Should I use the patch to generate a gromacs topology from psf file ?
I have NAMD created.coor and .vel files that have the final coordinates and
velocities. Also I have a dcd trajectory file. And according to these
informations what is the next step after getting the gromacs topology file to
continue a NAMD simulation in Gromacs ? What should I do ?
Kind regards.
--- On Thu, 9/30/10, Roland Schulz <rol...@utk.edu> wrote:
From: Roland Schulz <rol...@utk.edu>
Subject: Re: NAMD simulation in Gromacs
To: "oguz gurbulak" <gurbulako...@yahoo.com>, "Discussion list for GROMACS
users" <gmx-users@gromacs.org>
Date: Thursday, September 30, 2010, 6:28 PM
Oguz,
On Thu, Sep 30, 2010 at 4:52 PM, oguz gurbulak <gurbulako...@yahoo.com> 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
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