AMBER Archive (2003)

Subject: AMBER: HB dynamics in water and Ion solvation free energies

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Tue Jul 22 2003 - 17:09:41 CDT

Hi amber users,

I have two questions:
1. What is the way to characterize the dynamics of formation and breaking
of HB in water. Is there a way to analyze a trajectory files and obtain
such information?

2. What is the best way to estimate absolute free energies of hydration
for a given ion (the way defined by Aqvist): Delphi, Gibbs, ...which
module?

Thank you,
Ioana

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