[gmx-users] Thermostats and MSD

[Michael Shirts]

For #1, see: http://pubs.acs.org/doi/abs/10.1021/ct400109a

For #2, I think you'll have to figure that out for yourself.

On Wed, Mar 11, 2015 at 5:42 AM, sujithkakkat . <sujithks58 at gmail.com>
wrote:

> 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.
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