Fro the majority of the analisys implemented in gromacs, you don't
need the tpr, a pdb and the xtc are ok.
If you use the latest gromacs version (4.5.1) you need only the pdb
because gromacs is able to read each format vmd is able to read.
To enable this feature, you have:
1.Compiling gromacs with the flags "-L/usr/lib -ldl"
2.At runtime setting the VMD_PLUGIN_PATH to the sub-directory molfile of VMD
If you do this, you can do:
trjconv -f trajectpry.dcd -s file.pdb ........
and the same with each tools
Regarding conversion, I think editconf is the bestsolution
Il 30/09/2010 22:57, oguz gurbulak ha scritto:
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, Roland Schulz /<rol...@utk.edu>/* wrote:
From: Roland Schulz <rol...@utk.edu>
Subject: Re: [gmx-users] NAMD simulation in Gromacs
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Date: Thursday, September 30, 2010, 10:13 AM
On Thu, Sep 30, 2010 at 7:55 AM, Mark Abraham
<mark.abra...@anu.edu.au
<http://us.mc363.mail.yahoo.com/mc/compose?to=mark.abra...@anu.edu.au>>
wrote:
----- Original Message -----
From: oguz gurbulak <gurbulako...@yahoo.com
<http://us.mc363.mail.yahoo.com/mc/compose?to=gurbulako...@yahoo.com>>
Date: Thursday, September 30, 2010 21:38
Subject: [gmx-users] NAMD simulation in Gromacs
To: gmx-users@gromacs.org
<http://us.mc363.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org>
> Dear All,
> I performed a 50 ns md simulation using NAMD and want to
continue this simulation for 10 ns in Gromacs. Is it possible
to continue a NAMD simulation in Gromacs ? If so, could you
please give me the information about this process ?
Not really. You would need to generate a .top in the normal
way, and this process cannot use any topology information that
NAMD was using. You could start the GROMACS simulation from
the endpoint of the NAMD simulation, but it would not be
continuous in any sense.
We have a patch to psfgen to generate gromacs topology. We plan to
put this on our website. While it hasn't be uploaded yet, please
write me in case you would like to have a copy. It does convert
the parameter files. We use Pär's scripts to do that part.
Secondly can I convert NAMD output files into gromacs output
files and use gromacs analysis tools ? Could you please also
give me the information about this issue ?
If you have VMD installed then GROMACS is supposed to be able
to link to its libraries to enable GROMACS tools to read any
file format that VMD can read, which will include all NAMD
formats. I'm unaware that anybody has written any
documentation about this, however. That's probably the path of
least resistance.
Yes as long as VMD is installed (and GROMACS is compiled with
DLOPEN support - which is default) all the GROMACS tools
automatically can read most VMD supported format. The exception is
any format which doesn't record the number of atoms (as e.g. Amber).
Roland
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