[gmx-users] viscosity and surface tension

[David van der Spoel]

On 25/11/16 21:21, Andrew Bostick wrote:
> Dear gromacs users,
>
> How to calculate viscosity and surface tension in the simulation of some
> small molecules in the box of water.
>
> Best,
> Andrew
>
Surface tension is done by extending the box with vacuum, at least twice 
the amount of volume, running a simulation and then extracting the 
number out the energy file. You may have problems equilibrating if the 
concentration is low.

Viscosity, please check the pdf manual, there are some methods but it is 
not easy due to sampling.

-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se