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, Saumyak On 2 May 2017 at 10:33, David van der Spoel <sp...@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 > -- > 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-requ...@gromacs.org. > -- ================================ *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 : saumyakmukher...@gmail.com smukher...@sscu.iisc.ernet.in ================================ -- 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-requ...@gromacs.org.