[gmx-users] Re: PMF calculation between protein and ligand

Thomas Schlesier schlesi at uni-mainz.de
Thu May 2 11:30:28 CEST 2013

If you refer to Justin's tutorial, you can use it for every system, 
where the reaction coordinate is the distane between two parts of the 
system. You probably need to make some little adjustments, but in the 
end it doesn't matter if you pull two proteins apart, or protein+ligand, 
2 water molecules, or even streth a protein.

Am 02.05.2013 08:59, schrieb gmx-users-request at gromacs.org:
> Sir
> I have query as to how to go ahead for potential mean force (PMF)
> calculation between protein and ligand. As per the umbrella sampling
> protocol you have provided us in gromacs tutotrial it says it is for
> protein molecules...

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