[gmx-users] gmxcheck and trjconv
tsjerkw at gmail.com
Wed Mar 7 17:56:55 CET 2007
Also note that you have 70 FRAMES with 1 ps time step. That means,
with the first frame at t=0, that you have a maximum time of (70-1)*1
ps = 69 ps in the output.
On 3/7/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> andrea spitaleri wrote:
> > Hi,
> > however in md0.log the right time is reported (69 and not 70)
> > and
> > David van der Spoel wrote:
> >> andrea spitaleri wrote:
> >>> Hi all,
> >>> silly question. I have checked a trr with gmxcheck and I get this
> >>> output below:
> >>> Item #frames Timestep (ps)
> >>> Step 70 1
> >>> Time 70 1
> >>> Lambda 70 1
> >>> Coords 70 1
> >>> Velocities 24 3
> >>> Forces 0
> >>> Box 70 1
> >>> however if then i use trjconv to dump a configuration file at 70 ps it
> >>> says:
> >>> WARNING no output, trajectory ended at 69
> >>> Is it normal? I don't mind to extract a configuration file at 69 ps,
> >>> however i was wondering if this
> >>> behaviour is normal or whether it is bug.
> >>> thanks in advance
> >>> Regards
> >>> andrea
> >> is the simulation still running? then file buffering may play in. alt.
> >> if you kill -9 then the buffers will not be flushed.
> buffering is separate per file. in trr you have only half a frame.
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
3584 CH Utrecht
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