[gmx-users] NAMD simulation in Gromacs

Francesco Oteri francesco.oteri at gmail.com
Thu Sep 30 23:23:32 CEST 2010

  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 /<roland at utk.edu>/* wrote:
>     From: Roland Schulz <roland at utk.edu>
>     Subject: Re: [gmx-users] NAMD simulation in Gromacs
>     To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>     Date: Thursday, September 30, 2010, 10:13 AM
>     On Thu, Sep 30, 2010 at 7:55 AM, Mark Abraham
>     <mark.abraham at anu.edu.au
>     <http://us.mc363.mail.yahoo.com/mc/compose?to=mark.abraham@anu.edu.au>>
>     wrote:
>         ----- Original Message -----
>         From: oguz gurbulak <gurbulakoguz at yahoo.com
>         <http://us.mc363.mail.yahoo.com/mc/compose?to=gurbulakoguz@yahoo.com>>
>         Date: Thursday, September 30, 2010 21:38
>         Subject: [gmx-users] NAMD simulation in Gromacs
>         To: gmx-users at gromacs.org
>         <http://us.mc363.mail.yahoo.com/mc/compose?to=gmx-users@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
>     -----Inline Attachment Follows-----
>     -- 
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