[gmx-developers] rerun thermostated
hessb at mpip-mainz.mpg.de
Tue Aug 9 13:58:25 CEST 2005
Michel Cuendet wrote:
> I just found out that when you rerun a trajectory with NH thermostats
> on, they actually rescale the velocities found in the trr file. This
> means that the temperature and pressure measured on reruns are
> incorrect. I used mdrun 3.3b (and grompp 3.2.1).
The rerun should be thermostatted, but of course in the proper way.
The 3.3 version uses a reversible NH integrator, so all the state
should be present in the trr file and the scaling could work correctly.
I also thought it would be, but maybe it is not.
Are both the run and the rerun done with 3.3?
> It is probably an easy fix to disable all thermostats and barostats by
> default with -rerun. Also, the averages are weird. nstenergy should be
> automatically set to 1, and the number of steps taken from the
> trajectory and not from the tpr file.
But fixing the averages is not trivial as you don't know beforehand what
steps between frames are (they are also not necessarily constant).
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