[gmx-developers] rerun thermostated

Michel Cuendet michel.cuendet at epfl.ch
Tue Aug 9 12:54:42 CEST 2005


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.



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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