[gmx-users] PMF Profiles using Free Energy Perturbation(FEP) method.

Kim Q Hwan kim.qhwan at gmail.com
Mon Oct 13 16:01:49 CEST 2014

Dear all, 

I simulated two solid crystals and water system. The solid crystals solvated in the bulk water. I want to calculate the potential of mean force(PMF) between two solvated solid crystals.

For simplifying  question, I use only two snapshots, where two solids have 3nm and 3.02nm distance each. Due to confined water in 3nm distance is too bulk like, the free energy difference dG between 3nm and 3.02nm should be almost 0.

In each snapshot, I carried out different simulation. Distance between two solids is constrained by the pull=constraint method and I check the distance(t). I get two energy file, md0.edr md1.edr.

I calculate free enrgy difference dG=-kT*ln(<exp(-(E_B-E_A)/kT)>_A. And this is supported from g_energy util via -f2 flag:
 g_energy -f md0.edr -f2 md1.edr -ravg dg.xvg
option : 9 Potential

but resulting dF=-inf and this makes no sense in assumption.
I have questions about reason.

Thank you 

Kim Q Hwan
Center of Nano-Liquid
Department of Physics & Astronomy
Seoul National University
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