[gmx-users] dcd to gro!

Erik Lindahl lindahl at stanford.edu
Tue May 20 07:29:00 CEST 2003

Hi Swetha,

No, Gromacs files are portable across different CPUs and floating-point 

This sounds more like a bug in the MDtools package. Try the 'gmxdump' 
utility just to check that the file can be read. If not, it was written 
in a broken way.

The easiest way might be to write e.g. pdb files from Charmm, which can 
be read directly by the Gromacs tools. (a trajectory with multiple 
frames in a single pdb file is ok).



On Tuesday, May 20, 2003, at 10:49  AM, Swetha Vijayakrishan wrote:

> hi gromacs users,
> i ran an MD simulation with the Charmm software.This simulation was 
> run on
> the HP Alphaserver ES-45 ( Compaq Alpha ).
> I then converted the dcd file obtainded, to the trr format by using the
> Trio software , which is a part of the MDtools package of the univ of
> illinois,urbana campaign.
> Now i tried using this converted trr file for analysis in gromacs.
> when i tried the g_rms command i.e
> g_rms -s x.pdb -f x.trr -o rmsd.xvg
> i got the following error:
> Warning: can not make broken molecules whole without a run input file,
>          don't worry, mdrun doesn't write broken molecules

More information about the gromacs.org_gmx-users mailing list