[gmx-users] Split pmf

Jochen Hub jochen at xray.bmc.uu.se
Mon Oct 4 09:56:14 CEST 2010

  On 10/2/10 Oct 2,10:51 PM, Петр Попов wrote:
> Hello, dears gmx-users!
> I posted a message, but didn't get a response, it was my first one, so 
> may be I did something wrong. Anyway, here it is:
> I've already run md and got pmf and it's correct. But I want to get 
> not just a pmf of total force, but several profiles each of which 
> corresponds to the different components. For example, one pmf - 
> protein-protein interactions, another - protein-solvent interactions. 
> Or another, one pmf corresponds to electrostatic, another to VdW etc.
> Should I change a program's code? If so, tell me please in what 
> exactly program?
> Or may be gromacs have similar functions? Or is the another way to 
> split pmf?
Hi, what we did some years ago (Hub and de Groot, Does CO2 permeate 
through aquaporin-1, Biophys J 91, 842-848 (2006)), we used the energy 
file to decompose the potential (that is the enthalpic contribution to 
the PMF) into solute-water, solute-protein interactions, etc. You would 
have to make a tpr file with different energy groups and then do a 
rerun. Note that we do not decompose the mean force with that procedure 

I hope this helps.



> Thank you for your attention!

Dr. Jochen Hub
Computational and Systems Biology
Dept. of Cell&  Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4715056 Fax: +46-18-511755

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