[gmx-users] Use of gmx select

[Nicolas Cheron]

Dear all,

I am a little bit lost with the use of select. I would like to count how
many water molecules there are within 3Angstrom of a protein. I first used
the following command to count the oxygen atoms:

gmx select -s File.gro -f File.xtc -n Index.ndx -os Wat-0.3.xvg -xvg none
-select "name OW and within 0.3 of group Protein"

Then I wanted to count for the center of mass with:

gmx select -s File.gro -f File.xtc -n Index.ndx -os Wat-0.3.xvg -xvg none
-select "res_com of resname SOL and within 0.3 of group Protein"

I have found significantly different values (in the order of 20%) which
surprises me. Can you please confirm me that the last command is correct,
and if not tell me what would be the correct use of select to count the
number of water molecules that have their center of mass within 0.3nm of
the protein.

Thank you

Nicolas