[gmx-users] Re: NAMD simulation in Gromacs

oguz gurbulak gurbulakoguz at yahoo.com
Sat Oct 2 16:18:57 CEST 2010

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 <roland at utk.edu> wrote:

From: Roland Schulz <roland at utk.edu>
Subject: Re: NAMD simulation in Gromacs
To: "oguz gurbulak" <gurbulakoguz at yahoo.com>, "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Thursday, September 30, 2010, 6:28 PM


On Thu, Sep 30, 2010 at 4:52 PM, oguz gurbulak <gurbulakoguz at 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.


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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