Re: NAMD and Gromacs

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Thu Sep 30 2010 - 17:02:04 CDT

Hi,

The easiest way I found is to do it component-wisely.

Suppose, you have protein+membrane+water+ion in your system.
1): Use VMD script to save your system into individual pdbs, like,
protein.pdb, membrane.pdb, water.pdb, ion.pdb
2):
a: use gromacs pdb2gmx to generate topology for protein, membrane. If
you want to use force field like CHARMM, AMBER, this should be
straightforward. However, if you prefer OPLS, then some tricks are
needed to convert the lipid molecules.
b: use gromacs editconf to convert water.pdb, ion.pdb to *.gro files.
Here you need to change the names like TIP3 to SOL, OH2 to HW2, etc.
3): Now you can simply cat all the components in gro format into a
united file. Then include the protein, membrane topologies into the
system topology file.
4): Done.

Hope this helps,
Bin

On Sep 30, 2010, at 2:06 PM, oguz gurbulak wrote:

> 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 Iím 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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