VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Sep 05 2009 - 14:45:59 CDT

On Fri, 2009-09-04 at 09:49 -0500, John Stone wrote:
> Hi,
> We don't have a gromacs plugin for reading the .itp or .top files,
> so you'd either need to translate your structure into a PSF or some
> other bond-specifying file format for which a VMD plugin exists,

for the conversion to .psf there is this script in the vmd script
library. not sure whether this is still working, but a prerequisite
is that one generates a "preprocessed" .top file when generating
the .tpr file with grompp (-pp flag).
http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/top2psf/

> or someone would need to write a VMD plugin to read these other gromacs
> file types. If someone is interested in writing a VMD plugin for reading
> more of the gromacs related files, I would be happy to provide assistance
> and help get it going.

the flexible nature of the gromacs topology format would make it
rather difficult to interface it with the molfile library. it would
probably be much easier to integrate the functionality of top2psf
into the topotools package, at least this is my plan for the not
so far future. the dependency on running the preprocessor cannot be
avoided but since topotools is written in tcl script, there is more
flexibility to provide additional information to the file reader
about how and where to find the gromacs installation and the required
include files to have VMD run the preprocessor. similarly, the plan
is to add a tool that would allow VMD to _write_ gromacs .top files,
at least up to the level that it would be possible to use gromacs'
analysis tools. not sure how much effort it would be to generate
complete .top files for MD.

cheers,
    axel.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Sep 02, 2009 at 05:52:23PM -0400, BAN,YOUNG MIN wrote:
> > Hello.
> >
> > I am trying to represent DPPC lipids as bonds or lines. But since
> > I am using Marrink's coarse grained model, it seems that vmd does
> > not recognize bonding between coarse grained molecules. I am using
> > Gromacs, so I have .gro, .itp, and .top files.
> >
> > How can the lipids be represented by bonds or lines using those
> > .gro, .itp, or .top files? Do I need other type of files to do
> > this?
> >
> > Thanks in advance.
> >
> > Young-Min Ban
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com 
Research Associate Professor
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.