[gmx-users] Regrading trn file and CPU usage

David spoel at xray.bmc.uu.se
Wed Apr 13 19:07:41 CEST 2005

On Thu, 2005-04-14 at 17:51 +0300, Itamar Kass wrote:
>    Hi all, I wish to bid together two things wish bother me. The first 
> one regard trn file: I did 0.5ns simulation of a system which I have to 
> analysis using a very small step and with good statistics. Due to those 
> factors I saved snapshots every 10 step, with time step 5fs. I got HUGE 
> trr file (~57GB), but the simulation ended gracefully (I have OSX).
> Trying to run analysis on this file I got from the program the next line:
>    /Fatal error: Can not determine precision of trn file/
Have you tried running gmxcheck?
If the file is not corrupt this means you have a first frame without
x,v,f or box. Which is basically impossible. Are you sure this is not an
xtc file which has been renamed?

> Does someone know of a way to overcome it?
> My second question is more theoretic, I have one CPU for a MD run, what 
> will be more efficient (i) run the MD as a single process on this CPU or 
> (ii) run the MD as two or more processes on this single CPU. This can be 
> widen to the question is it more efficient to have more processes then 
> CPU for the same MD run?
No, never. 
> thanks you all, Itamar.
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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://xray.bmc.uu.se/~spoel

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