[gmx-users] Help needed using gmx select of GROMACS

Budheswar Dehury bude at kemi.dtu.dk
Thu Mar 28 13:55:12 CET 2019

Dear Gromacs Developers and Users,
I need a small help in GROMACS trajectory analysis. I want to define a selection i.e., 4Ang volume around two residues (from different chains X  and chain Y ) that make your binding site --- Within this selection I want count number of waters molecules along the trajectory (it's a lipid bilayer system with TIP3P and POPC).

How can I estimate the number of water molecules using gmx select and gmx dist or gmx mindist..through gromacs or VMD.

Looking forward to hear from you

Thanking You
Sincere Regards



Budheswar Dehury


bude at kemi.dtu.dk<mailto:bude at kemi.dtu.dk>


Building 206

2800 Kgs. Lyngby


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