[gmx-users] Energy/temperature drifts in Gromacs 4.0 / inconsistencies with Gromacs 3.3.1

Pietro Amodeo pamodeo at icmib.na.cnr.it
Fri Mar 13 20:02:40 CET 2009

> That was a long mail. How about T-coupling? Which algorithm did you use?

Sorry for the long mail. For T-coupling I used Berendsen al gorithm.

> Did you do a diff on the md.log to check for differences in the mdp
> parameters?

Yes, I attach the diff file (emended of references and other comments), as
well as the run parameters reported in the NEW md log file.
For system 1 I tried both the same tpr file (from 3.3.1) in 3.3.1 and
4.0.4 simulations, and a new 4.0.4 format tpr file with grompp for 4.0.4
md run, but all simulations stopped in about 2,000 steps.
System 2, for which I attached the different parts of the log files, was
simulated using the same tpr file (from 3.3.1) for both 3.3.1 and 4.0.4 MD

> Did you run these in parallel? What happens when you run it
> sequentially? And what happens in single precision?

For system 1, changing precision, compiler or serial-vs-parallel run only
affect the exact step at which the simulation stops. Also for system 2
these parameters do not affect the overall oscillating behaviour of the


Dr. Pietro Amodeo, PhD.
Istituto di Chimica Biomolecolare del CNR
Comprensorio "A. Olivetti", Edificio 70
Via Campi Flegrei 34
I-80078 Pozzuoli (Napoli) - Italy
Phone      +39-0818675072
Fax        +39-0818041770
Email    pamodeo at icmib.na.cnr.it
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