[gmx-developers] rerun thermostated

[Michel Cuendet]

Hi

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).

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.

Ciao,

Michel

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Michel Cuendet, Ph.D. student
Laboratory of Computational Biochemistry and Chemistry
Swiss Federal Institute of Technology in Lausanne (EPFL)
CH-1015 Lausanne						
Switzerland                            Phone : +41 21 693 0324
lcbcpc21.epfl.ch/~mitch	                       +41  1 633 4194
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