[gmx-users] mdrun -rerun with gmx3.2 and gmx3.3

Mark Abraham Mark.Abraham at anu.edu.au
Tue Mar 21 05:56:30 CET 2006

Xavier Periole wrote:
> The energies indicate that:
> 0) I see a systematic difference with the original energies (not 
> significant), but using
> the trr file helps getting better.
> 1) I do not see ANY difference between the rerun using the two tpr file 
> (Unexpected ?!?!)
> 2) I do not see significant differences between gmx3.2 and gmx3.3 (New 
> ?!?!) in all cases.
> 3) I see significant differences in energies when generated with xtc and 
> trr files (New ?!?!).
> trr files help.
> All this seems in agreement with the past remarks of David and Mickael 
> until I compare
> the energies obtained with the twp tpr files ?! Am I missing something ?
> Note that my system is quite big (in cubic (!) box about 12.0, 12.0, 
> 8.0, in nm).
> Does this make sense to any of you ?

I'm having difficulty understanding what you've done, but some things 
that might help you understand what you've done are

1) The .trr and .xtc versions of the trajectories will correspond to 
slightly different positions and so you should expect slightly different 
energies to result
2) You need to use .edr files with grompp/tpbconv for exact restarts to 
be exact
3) Different versions of the mdrun code should be expected to be 
slightly different. A default value of a parameter may have changed, of 
course, but in general the execution order of the two versions need not 
be the same. If you add up a few thousand floating point numbers in a 
slightly different order you will get different results. Evaluation of 
LJ and Coulomb terms requires this.
4) Different versions may produce identical .tpr files, or might not. 
You can check this with gmxdump.


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