[gmx-users] g_select syntax

Bin Liu fdusuperstring at gmail.com
Wed Sep 3 22:32:28 CEST 2014

Dear Teemu,

Thank you for your explanation. Now I understand why the first selection
gives more residues as it's simply a superset of the second selection. I
just realized to accomplish what I initially want, i.e., to obtain the
residue index list of LIPID whose center of mass is within 1.0 nm of the
surface of protein, I just need

group "LIPID" and res_com within 1.0 of group "PROTEIN"
 g_select -sf selection.dat -f traj.trr -s traj.tpr -n system.ndx  -oi
index.dat -seltype res_com -selrpos atom

Again, I am a bit confused by that it seems the sole function of -seltype
res_com is outputting residue index instead of atom index. If I use
-seltype atom instead, g_select will return all the corresponding atoms in
the residues selected by the selection just above. What frustrates me most
is I can't find a flag to be used in selection.dat to let g_select output
residue index, not atom index.

Best Regards,


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