Hi,
I think I got it :-) Using gmx 3.3.1 with the same thermostat and barostat settings as the original run, I get the right LJ energies within 0.1%. I used tcoupl and pcoupl = "no" because I somehow remembered that thermostats could do weird things when rerunning (see the old thread : http://www.gromacs.org/pipermail/gmx-developers/2005-August/001290.html )
But apparently the box is not reread form the trajectory if the pcoupl option is deactivated. It would be much safer for users if the appropriate options were automatically set when -rerun in invoked:
nstlist = 1 nstenergy = 1 NO rescaling of velocities NO rescaling of box size Do read the box sizes from the trajectory Cheers, Michel ========================================================== Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne, Switzerland www.isb-sib.ch/groups/Molecular_Modeling.htm ==========================================================
LJ-rerun.eps
Description: PostScript document
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