[gmx-users] Calculation of volume of protein hydration layer

David van der Spoel spoel at xray.bmc.uu.se
Tue May 2 07:03:28 CEST 2017

On 01/05/17 18:44, Saumyak Mukherjee wrote:
> Dear Users,
> Can anybody please tell me how to calculate the volume of protein hydration
> layer as a function of time? Apart from this I would also like to calculate
> the volume of second hydration shell around a protein.
> I can define hydration layer in two ways:
> 1. g_select
> 2. trjorder
> If this calculation is possible in GROMACS, please guide me how to do it.
> Thanks in advance,
> Saumyak
You may also have a look at gmx freevolume to compute the volume inside 
a group. Not sure how well it works and whether you could do the 
selection at once.

Then I think you should ask yourself what in particular the second 
hydration layer means and whether you can unambiguously define such a thing.

David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.

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