[gmx-users] Water permeation through a channel of membrane protein (Naba)

[Joel Janke]

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-request at maillist.sys.kth.se wrote:
> 
> Water permeation through a channel of membrane protein (Naba)