Hello everyone
I am following the Justin Lemkul's tutorial for Umbrella sampling:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html
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.
Cheers!
Martin
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