[gmx-users] hydrophobic interactions

[David van der Spoel]

On 11/01/16 17:54, Justin Lemkul wrote:
>
>
> On 1/11/16 11:53 AM, Chiara Bello wrote:
>> Dear gromacs users,
>>
>> I am interested in quantify the intermolecolar hydrophobic
>> interactions of my aggregating system over the trajectories. Is it
>> possible in gromacs?
>>
>
> Of course. But you need to define what you want to quantify. Contact,
> SASA, etc. are all easily calculated using existing analysis tools.
>
> -Justin
>
You can indeed quantify these things but they are not hydrophobic 
interactions. Hydrophobic interactions (and forces) do not exist. There 
is something called the hydrophobic effect though. See e.g. 
http://pubs.acs.org/doi/abs/10.1021/jp015514e

-- 
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