VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Feb 26 2013 - 08:30:15 CST

To me that looks like something that the Gromacs tool is unhappy about
with regard to timestep timestamps or something similar. Catdcd only has
some of the information that Gromacs may want/need/expect, so it may not
be able to make a TRR file that completely satisfies the Gromacs tools
without further manipulations. The DCD format used by NAMD is very
minimalistic, and there are quite a few things it doesn't contain that
the Gromacs tools may be expecting.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Feb 26, 2013 at 03:29:34PM +0530, manali_at_bioinfo.net.in wrote:
> Hi,
>
> I have a big trajectory file (18G) in dcd format generated by NAMD, that i
> would like to convert to xtc format.
> The way i tried it was to convert it from dcd to trr and then use trjconv
> for trr to xtc, however this fails, giving error:
>
> Last frame -1 time 0.000
> Setting output precision to 0.001 (nm)
> WARNING no output, last frame read at t=0
>
> When i run a "gmxcheck -f traj.trr" it shows error:
> Checking file traj.trr
> Last frame -1 time 0.000
> # Atoms -1
> Last frame -1 time 0.000
> Item #frames Timestep (ps)
> Step 0
> Time 0
> Lambda 0
> Coords 0
> Velocities 0
> Forces 0
> Box 0
>
>
> Is the catdcd not writing out properly or am i missing a key command in
> gromacs to set the timestep?
>
> Thanks in advance,
> Manali
>
>
> --
> Manali Joshi, Ph.D.
> 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078