[gmx-users] Regrading trn file and CPU usage

[Itamar Kass]

   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/

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?


thanks you all, Itamar.