[gmx-users] Free energy between surfaces

Jianguo Li ljggmx at yahoo.com.sg
Sat Feb 18 10:42:00 CET 2012

One way to get the free energy is to measure the force as a function of distance and do the integration to get the PMF, as used in the paper: 

Ronen Zangi, Morten Hagen, and B. J. Berne. 2007. Effect of Ions on the Hydrophobic Interaction betweenTwo Plates. J. AM. CHEM. SOC. 2007, 129, 4678-4686


 From: Steven Neumann <s.neumann08 at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Saturday, 18 February 2012, 17:25
Subject: [gmx-users] Free energy between surfaces

Dear Gmx Users,

I am wondering whether you know a technique for calculating the free energy between charged surfaces - I want to calculate distance when the deltaG=0 so that the surfaces are in equilibrium - closer distance will make that they repeal each other, longer (deltaG<0). Will Umbrella Samling would be ok for those calculations? If I pull a whole surface away from another (in NPT) the box vectors will descrease to maintain the same density of water. Thus, the surface will be smaller, am I right? How about pbc?

If you have any ideas, please share!


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