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

[Budheswar Dehury]

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

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Budheswar Dehury

Postdoc



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