[gmx-users] Re: mdrun -rerun and box size bug not fixed?

Michel Cuendet michel.cuendet at isb-sib.ch
Tue Nov 6 14:12:29 CET 2007


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



Michel Cuendet, Ph.D
Molecular Modeling Group
Swiss Institute of Bioinformatics
CH-1015 Lausanne, Switzerland

-------------- next part --------------
A non-text attachment was scrubbed...
Name: LJ-rerun.eps
Type: application/postscript
Size: 23174 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20071106/0753f22a/attachment.eps>

More information about the gromacs.org_gmx-users mailing list