[gmx-users] Identical energies generated in a rerun calculation ... but ...

Luca Mollica mollica.luca at hsr.it
Wed Apr 22 12:44:09 CEST 2009

Dear users,

I am experiencing some troubles in using GMX 4.0.4 trying to rerun trajectories and obtaining energies 
for single residues and/or portion of proteins. According to the mdrun command help and to my experience 
with the previous versions of GROMACS, I have edited my mdp file including the desired groups for energy 
calculation, grompped it and reruned the previous calculation with the "original" trr trajectory.
I have noticed a different behaviour of mdrun plus -rerun flag between the usage of a single CPU or the 
original number of CPU used in the production run: that is, in the original production run I have used 24 
CPU (12 for PME, nosum flag used), in the trajectory rerun step I have tried to use both 24 CPU or single 
CPU and the result was different and in the case of parallel run "strange". The parallel rerun energy 
file led to an energy file made of a column of the same number, whereas the single CPU one led to a 
normal energy trend vs time: interestingly, the first value of this last calculation coincided with the 
one repeated in the previous "strange" file.
Hence, the single CPU recalculation works correctly, despite the fact that (as expected) it takes longer 
time for huge trajectories with respect to parallel run: but what's wrong with parallel rerun ? Is it a 
bug of the newer version of the code or am I missing something in the comprehnsion of how the rerun issue 
is working at code level ? It seems to be more likely a code bug ... but I wait for your comments and/or 

Thanx in advance



Luca Mollica
Biomolecular NMR Laboratory 1B4
Dulbecco Telethon Institute c/o S. Raffaele Scientific Institute
Via Olgettina 58
20132 Milano

mollica.luca at hsr.it; lucamollica at gmail.com

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