[gmx-users] Umbrella sampling sanity check

[Nash, Anthony]

Hi all,

I would appreciate a little sanity check for umbrella sampling pull code
parameters.

My reaction coordinate is defined as the distance between a globular
soluble enzyme and a substrate in solution (water). I have already
captured the individual windows using the trajectory generated from an
earlier meta-dynamics simulation. I would now like to perform umbrella
sampling, a technique which I feel is more accountable for the free
energies it generates once a reaction coordinate is known.

My two questions:
1) My earlier meta-dynamics simulation used the distance between the
enzyme active site zinc ion to a particular substrate atom. The substrate
atom (a backbone carbonyl oxygen) would in reality coordinate with the
zinc prior to proteolysis. In pull code, can pull_group0 and pull_group1
simply be the same two atoms (Zn2+ and O)? As the distance harmonic
potential works on COM, this would just be a point of an atoms.
     
2) Up until now I¹ve always worked on bilayer, so forgive the simplicity.
Given that my substrate could diffuse in any direction, should I set
pull_dim=Y Y Y?

Many thanks
Anthony

Dr Anthony Nash
Department of Chemistry
University College London



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