Hi Naba, It sounds like you almost have the solution to your problem. I would recommend using trjorder to count the waters in the channel.
Good luck. # make an index file with the channel protein residues echo -e "r 65 | r 66 | r 68 | r 70 | r 73 | r 74 | r 77 | r 83 | r 91 | \n name 24 channel \n q " | make_ndx -f production100mM.gro -o index.ndx # Count the water molecules within 3.5 angstroms of the channel protein residues echo "channel \n Water \n q" | trjorder -f production100mM.gro -s production100mM.gro -n index.ndx -nshell waters_in_channel.xvg -r 0.35 > On Feb 5, 2019, at 6:00 AM, gromacs.org_gmx-users-requ...@maillist.sys.kth.se > wrote: > > Water permeation through a channel of membrane protein (Naba) -- 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.
