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

Xavier Periole x.periole at rug.nl
Mon Mar 20 16:18:10 CET 2006


I have reruning simulations using gmx3.2 and found out some deferences
between the original and rerun energies. I found the posts made by David
Mobley and Mickael Shirts about this issue. Accordingly I downloaded
gmx3.3 and compiled it with the fixed md.c for the rerun, found in the
bugzila page (thanks to D. Mobley for the info).

The present email is about the fact that I see differences between the 
energies and the rerun ones but in a different manner as previously 
I'd like to understand the reason of this.

 From this I have been reruning a piece of trajectory (first 200 ps)  
with gmx3.2. I rerun it on both trr and xtc files (generated with 
trjconv and the
original xtc and trr files), using gmx3.3 (with the md.c fixed) and gmx3.2,
and using tpr files build with gmx3.2 with the initial coordinate file 
and the final
coordinate file, and the same mdp file (including: nstenergy = 1).

The corresponding energies are in the attached file for the original 
energy file
and the 8 reruns performed.

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 ?


 Xavier Periole - Ph.D.

 Dept. of Biophysical Chemistry / MD Group   
 Univ. of Groningen
 Nijenborgh 4
 9747 AG Groningen
 The Netherlands
 Tel: +31-503634329
 Fax: +31-503634398
 email: x.periole at rug.nl
 web-page: http://md.chem.rug.nl/~periole

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