[gmx-users] REMD analysis

[Kalyanashis Jana]

Dear all,

I have performed an REMD simulation for protein drug system (8350 + 32500
sol) using gromacs-4.4.5 package. But I could not understand how to do
analysis of REMD. I have used 10 set of replicas (298 K to 308.31K with
r=1.0038, the common ratio of the geometric progression)  for REMD
simulation and carried out a 5 ns simulation. I would like to compare the
thermodynamics of two drug molecules using REMD. Can you please suggest me,
how can I plot potential energy vs probability or how can I get free energy
profile? What types of analysis do I need to understand REMD?

Looking forward to hear from you.

Thanks in advance,

Kalyanashis Jana