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