[gmx-users] water molecules (interfacial)

leila karami karami.leila1 at gmail.com
Sun Nov 14 13:50:04 CET 2010

Dear gromacs users

I was trying to count waters involved in the interface between Protein_A and

I made a selection.dat file as follows:

waterO = group SOL and name OW;
heavy1 = group Protein_A and group "Protein-H";
heavy2 = group Protein_B and group "Protein-H";
inter = waterO and within 0.35 of heavy1 and within 0.35 of heavy2;

is my selection.dat file true?
I used g_select -f .xtc -s .tpr -n .ndx -os -oc -oi -om -on -sf
selection.dat but gromacs:
Nothing selected, finishing up.

when I used g_select -f .xtc -s .tpr -n .ndx -os -oc -oi -om -on -sf
selection.dat -select, what should be put in front of -select to avoid
Nothing selected, finishing up?
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