[gmx-users] PMF for membrane protein dimer

Ragnarok sdf fabracht1 at gmail.com
Thu Aug 13 04:21:43 CEST 2009

I am working with a membrane protein dimer, each monomer being
constituted of a single helix. I have already studied the effect of
point mutations on the structure and the free energy involved by using
FEP. But I have read a paper in which the author has done PMF
calculations in order to calculate the free energy of dimerization. In
this paper (ref J. Am. Chem. Soc., 2005, 127 (23), pp 8478–8484) the
author describes a system that is quite similar to mine, though he
uses NAMD to do obtain the trajectories. I have tried gathering some
information on this particular method (PMF) in gromacs and have found
very little information regarding PFM being used to separate protein
dimers or even separating system containing more than a dozen atoms or
so. If I understood correctly, I am supposed to pull the two
structures apart, and associate a lambda value for each distance I
obtain. Well, I am a little bit lost here, since I did not really
understand how is the pull code linked with the free energy
calculation. I even found the "two argon PMF" tutorial quite
confusing, since I do not see how I would obtain a restrain for the
monomers in such a big system.
So, for now I would like some information on how to obtain this kind
of practical information (tutorials, instructions, articles etc). I
know everyone is quite busy solving their own problems, so any
direction now would help me have more specific doubts so that I can
further address this list with more "useful" questions.
Thank you
Fabrício Bracht

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