From: oguz gurbulak (gurbulakoguz_at_yahoo.com)
Date: Thu Sep 30 2010 - 16:06:46 CDT
Dear All,
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
- 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.
-using VMD ( but I’m not sure if it works )
-using editconf in gromacs ( if you have the structure in pdb format, you can convert it into a .gro file with editconf. Also, the size of the box should be specified (in gromacs the length for the vectors a, b and c is in nm, not angstrom)
editconf -f file.pdb -o file.gro -box a b c -angles 90 90 90
Could you share your ideas about this process ? What should I do ?
Then I should convert the psf file into gromacs top file.
If I get a gro and top file correctly, I can continue NAMD simulation in Gromacs. Is it true ?
I examined the gromacs tutorials. And I think I must have a tpr and a xtc file to use gromacs analysis tools. I can get a xtc file from NAMD dcd file but how can I create a tpr file ? Is there a way to get a tpr file from NAMD files?
Kind regards.
--- On Thu, 9/30/10, Hannes Loeffler <Hannes.Loeffler_at_stfc.ac.uk> wrote:
From: Hannes Loeffler <Hannes.Loeffler_at_stfc.ac.uk>
Subject: Re: namd-l: NAMD and Gromacs
To: namd-l_at_ks.uiuc.edu
Date: Thursday, September 30, 2010, 10:26 AM
On Thu, 30 Sep 2010 14:55:48 +0200
Francesco Oteri <francesco.oteri_at_gmail.com> wrote:
> If you have the latest coordinates and velocities, you need to
> convert them into .gro file that can be used as restart for gromacs.
If the topology/structure file has been created with psfgen there may
be one complication: this program has the habit of reordering atom
numbers in cystines and the C-terminus, at least in the case of
X-PLOR/CHARMM topologies. But I just see that the question has also been
answered over in the Gromacs list. Somebody has a patch to psfgen to
directly generate Gromacs topologies.
Cheers,
Hannes.
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