[gmx-users] gmxcheck and trjconv
David van der Spoel
spoel at xray.bmc.uu.se
Wed Mar 7 14:55:02 CET 2007
andrea spitaleri wrote:
> however in md0.log the right time is reported (69 and not 70)
> 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
>>> 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
>> 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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