From: John Stone (
Date: Wed Sep 21 2005 - 14:27:45 CDT

  You can delete the duplicate frame if you want once the trajectory is
loaded. If we wrote the necessary topology reader plugins, you'd probably
be able to load the topology file and the trajectory and you'd no longer
have the duplicated frame if you just loaded those two files.
If you or others want to try out a Gromacs topology file reader plugin,
email me to let me know and I can provide you with test builds when I
get started on it.

  John Stone

On Wed, Sep 21, 2005 at 12:17:10PM -0700, Nathan C. Rockwell wrote:
> I'm another gromacs user! Although my only complaint on importing gromacs
> stuff is that working with the .gro and .trr (structure and trajectory,
> respectively) I haven't figured out how to avoid getting a duplicate frame
> from importing the trr, which is pretty close to the bottom of my list of
> things to do, much less anybody else's.
> In looking at the original message, I noticed a couple of questions about
> this specific case:
> 1. is this GROMOS or gromacs? They're not the same thing; gromacs just uses
> GROMOS force fields, among others.
> 2. gromacs (and maybe GROMOS) uses nm and not Angstroms as distance, so
> that's a frequent source of confusion when people try their own scripts.
> 3. at least on the mac, there are newline problems that confuse VMD if you
> use a word processor (as opposed to a text editor)--these typically manifest
> as weird bonding and missing atoms, etc.
> nr
> On 9/21/05 8:20 AM, "John Stone" <> wrote:
> >
> > Hi,
> > I looked at the Gromacs web site and it would seem that the ".dat" files
> > aren't a documented format at all. It's hard for me to say why your
> > conversion program doesn't work right, but if your main problem is that
> > you're getting incorrect bonding and such, this is probably simply an issue
> > of VMD being forced to guess bonds by a distance based bond search since
> > it isn't getting that information from your PDB file. The Gromacs web page
> > only had this to say about these .dat files:
> >
> >
> > If you have the structure in a normal Gromacs topology file, it would
> > probably be pretty easy to write a new Gromacs topology file reader
> > plugin that retrieves the correct bonding information and without having to
> > convert to a PDB file. If there are other Gromacs users on the VMD-L list
> > that would like to see VMD read more of the Gromacs files directly without
> > conversion, speak up now. What files do you guys want to be able to read?
> > If nobody wants new reader plugins I have plenty of other things to work on,
> > but this could probably be done in a day or two if there is sufficient demand.
> >
> > John Stone
> >
> >
> > On Wed, Sep 21, 2005 at 10:37:35AM -0400, Stanley Lan wrote:
> >> Hi everyone,
> >>
> >>> From Gromos output I got ***sxmd.dat (final coordinates) and ***rxmd1.dat,
> >> along with the topology file(***mta.dat). I tried to convert the final
> >> coordinates into pdb format and import it into VMD. It worked except the
> >> whole molecule is in pieces(broken bonds, mis-connected bonds). Same thing
> >> happend to other two visualization programs, PyMol and RasMol. I assumed
> >> it's because the final coordinats from GROMOS doensn't have the standard
> >> amino acid residues and the correct connection map. My boss didn't think
> >> so. He thinks there is something wrong with my conversion program and/or
> >> VMD.
> >>
> >> I try to prove he is wrong but I need to be able to import the gromos
> >> output files into VMD without conversion. Any comments/suggestions will be
> >> appreciated.
> >>
> >> Is there any GROMOS archive with string search function for me to search
> >> this kind of questions/answers?
> >>
> >> Ben.
> >>

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