[gmx-users] gmx select

Nicolas Cheron nicolas.cheron.boulot at gmail.com
Tue Nov 8 08:44:03 CET 2016

Dear all,

I am a little bit lost with the use of select. I am looking at a protein in
a water:glycerol mixture. I would like to count how many glycerol molecules
there are within 3Angstrom of the protein. I first used the following
command to count the central atom (named C2):

gmx select -s File.gro -f File.xtc -n Index.ndx -os Gly-0.3.xvg -xvg none
-select "name C2 and within 0.3 of group Protein"

This gives me on average over the trajectory 3.3. Then I wanted to count
for the center of mass of glycerols, which shouldn't be too far from the
central atom:

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

There I found 58.4. I got the same result with whole_res_com than with
res_com, and with Gromacs 5.1.1, 5.1.2 and 2016.

I am surprised by the difference. I suspect that the second command counts
all the atoms. Can someone please tell me if the last command is correct,
and if not tell me what would be the correct use of select to count the
number of center of mass of the glycerol molecules that have their center
of mass within 0.3nm of the protein.

Thank you


PS: I posted this question on the list a week ago but not sure it went
through, sorry for the double posting

More information about the gromacs.org_gmx-users mailing list