[gmx-users] Re: NAMD simulation in Gromacs

[Roland Schulz]

Oguz,

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.

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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