[gmx-users] calculation of potential and Sg

[Paymon Pirzadeh]

Hello,
I have a protein which has 4 Thr residues on its one side. I want to
calculate the potential energy and Sg of water molecules these Thr
residues are facing (up to 10 angstrom). I have a 10ns trajectory and I
might need only 5ns of it. How should I set my index file and which
tools will help me? Thanks in advance for your helps.
Regards,

Paymon