[gmx-users] Restraints influeincing free energy calculations

Nash, Anthony Anthony.Nash at warwick.ac.uk
Sun Jul 14 12:51:40 CEST 2013

Hi all,

Just a quick question - and perhaps some wisdom from those with more experience.

I am trying to use metadynamics with gromacs to plot an energy landscape about the rotation of two proteins. If I were to define my collective variables as ThetaA and ThetaB, Theta being the rotation about the protein principle axis, I could sample identical rotations but at different distances apart. Therefore, this introduces the idea of a third collective variable, absolute distance between the centre-of-mass of the proteins. Given that I don't actually want to sample space where these two proteins are beyond peptide-peptide interactions, it is of little interest plus would be extremely computationally crippling, I thought I could apply a restraint between the two proteins at a distance previously identified in literature using FRET. My two questions:

1) Would applying a restraint mess with or bias free energy calculations in any form of free energy calculations, be it, metadynamics or umbrella sampling, and,

2) words of wisdom from anyone who has undertaken such a problem?

Many thanks

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