[gmx-users] Calculation of volume of protein hydration layer
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
>> layer as a function of time? Apart from this I would also like to
>> 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,
>> 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
> 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.
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
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
More information about the gromacs.org_gmx-users