[gmx-developers] rerun thermostated

Michel Cuendet michel.cuendet at epfl.ch
Tue Aug 9 19:47:21 CEST 2005

Hi Berk,

Berk Hess wrote:

> The rerun should be thermostatted, but of course in the proper way.

No. I mean rerun with "mdrun -rerun traj.trr". Then the velocities are read at sparse timesteps, and they are not recalculated, and there is thus no reason to scale them. Whatever way the velocities in traj.trr were obtained, mdrun -rerun should take them as they are, and calculate the corresponding temperature, pressure, etc...

> Are both the run and the rerun done with 3.3?

No, but that was precisely the point : see what temperature 3.3 would give for velocities which 3.2 believed were at 300K. (answer: 303.47 K, see the other thread). If I leave the NH thermostat on in the mdp file for the rerun, the rerun gives me 303-something in the beginning of the trajectory, and as the thermostat momentum builds up, starts to scale the velocities back to 300 towards the end of the trajectory. These scaled velocites don't make any sense.



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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