[gmx-users] Thermostats and MSD

[sujithkakkat .]

Dear all,

  I am simulating a system of small hydrophobic solutes ( CH4)  dissolved
in water. Simulations are performed in the NPT simulation, and I would like
to determine the diffusion coefficients from MSD plots. I have two related
questions;

(1)  Is the thermostat going to seriously affect the diffusivity of the
molecules. I am using Nose-Hoover thermostat with a time constant of 0.2
ps. Is the choice of time constant very crucial while studying diffusivity.
Should I avoid thermostat and go for NVE simulations for studying
diffusivity.

(2) From radial distribution functions, it is found that there is
association between the hydrophobic solvents. I would like to know, if in
case a small cluster of the hydrophobic solutes are formed, then the
whether the rotational motion of these clusters contribute to dispalcement
in the MSD calculation.

Please comment.

Regards,
Sujith.