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

Saumyak Mukherjee mukherjee.saumyak50 at gmail.com
Wed May 3 00:30:44 CEST 2017

Dear Dr. Spoel

I have created a group in an index file for the hydration layer of water.
Now if I calculate the volume for this group using g_sas -tv flag from an
ordered trajectory (trjorder), will I get the correct volume (as a function
of time) of hydration layer?

Thanks and regards,

On 2 May 2017 at 10:33, David van der Spoel <spoel at xray.bmc.uu.se> wrote:

> 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.
> http://www.icm.uu.se
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*Saumyak Mukherjee*

Junior Research Fellow
Prof. Biman Bagchi's Group
Solid State and Structural Chemistry Unit
Indian Institute of Science
Bangalore - 560012

Mob : 8017292426
Alternative e-mail : saumyakmukherjee at gmail.com
                                smukherjee at sscu.iisc.ernet.in

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