[gmx-users] Umbrella sampling tutorial - V-rescale or Berendsen thermostat

Martin Nors Pedersen martin.pedersen at esrf.fr
Wed Nov 18 17:37:34 CET 2015

Hello everyone

I am following the Justin Lemkul's tutorial for Umbrella sampling: 

I am at the step where i want to perfom the NPT equilibration. Using the 
input file provided in the tutorial, I use grompp to prepare the .tpr 
file. I get a note, however, which states that the selected thermostat 
in the provided npt.mdp is not optimal:

     " The Berendsen thermostat does not generate the correct kinetic energy
      distribution. You might want to consider using the V-rescale 
thermostat. "

I just want to ask if there is some specific reason for choosing the 
Berendsen thermostat over of the V-rescale in the NPT equilibration? 
According to the manual ( 
http://manual.gromacs.org/online/mdp_opt.html#tc ), they are similar 
except for a stochastic term which makes the V-rescale thermostat 
better. But I do not know if this has any (significant) influence in the 
NPT equilibration.


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