From: Axel Kohlmeyer (
Date: Sun May 13 2007 - 14:46:04 CDT

On Sun, 13 May 2007, lnubiofox wrote:

YL> Dear users, I want to analysis the hydrogen bonds of a dcd file,
YL> unfortunately as far as I know there is no tools which can do this
YL> containing in vmd. At first ,I try to use gromacs

that is not entirely correct.

YL> instead,however,after I am familiar with it I found that gromacs
YL> cannot read dcd files and it is impossible to get the tpr file which
YL> gromacs needed to analysis. Is there any scripts which help us to
YL> get the occupancy of hydrogen bonds during the simulation ? Or is
YL> there any other ways to achieve this using vmd ? Any suggestions
YL> will be appreciated. Best regards, Yuan Liu Liaoning university

as you already noticed, the gromacs tools need a tpr file, i.e.
information about the elements (you can actually use VMD or catdcd
which uses the molefile plugins from VMD to convert .dcd into gromacs
supported .trr). the .dcd file contains nothing but the plain
coordinate information, so _no_ tool can analyse this without
additional knowledge about your simulation. the simples way to
make VMD aware of the elements would be to load a matching
.xyz or .pdb or similar file and then delete the frame(s), load
the .dcd(s) and do the analysis with 'measure hbonds'.
should be pretty straighforward. details on using measure hbonds
are in the VMD user's guide and several discussions about them
in the VMD-l mailing list archives.


YL> P.R.China

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.