[gmx-developers] renicing under windows, moving frozen atoms, some observations and a question

Michael Brunsteiner mbx0009 at yahoo.com
Thu Mar 25 10:31:08 CET 2004

dear all,


Does anybody know how I can put a job running on a windows
machine in the "background" so that the job continues running 
when I log off (as opposed to shut down) ??


1) A while ago i reported a bug in the umbrella code.
I tried the modification suggested Berk Hess in
and it worked fine for me.

2) I find that under certain conditions frozen atoms DO MOVE
in my simulations (NOT GOOD). This happens when I calculate a PMF
using constraints with the reference group consisting
of frozen atoms. The pull code seems to do something to the
the velocities or forces of the frozen atoms (evidenve
herefore is that the frozen atoms move only in the z-dimension
which is the pull dimension in my case). A while ago
Justin MacCallum wrote that the positions of the atoms ref group
are not modified by the pull code. Did this change, or is this maybe
a feature that generally occurs when constraining atoms in gromacs ??

3) I found that explicitely renicing a job under windows is 
generally not necessary, because if I start mdrun via a batch file
its priority as seen in the task manager is by default 
"low", i.e. the lowest possible on an 2000/XP machine
(which is what you'd want in most cases)


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