[gmx-users] Re: NAMD simulation in Gromacs

[Roland Schulz]

Oguz,

in case you want to try the psfgen patch, it is now available for download
on our group website at
http://cmb.ornl.gov/resources/developments/top-patch-for-psfgen

<http://cmb.ornl.gov/resources/developments/top-patch-for-psfgen>Roland

On Thu, Sep 30, 2010 at 7:28 PM, Roland Schulz <roland at utk.edu> wrote:

> 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
>



-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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