From: Ethan Croitoru (ecroitoru1_at_gmail.com)
Date: Wed Sep 09 2020 - 14:25:33 CDT
Hello,
I would like to use the DMRS colvar defined in this paper, *Convergence and
Sampling in Determining Free Energy Landscapes for Membrane Protein
Association*, by Domanski et. al. (
https://pubs.acs.org/doi/10.1021/acs.jpcb.6b08445) to do free energy
calculations on a TMD helical dimer, like their GpA example. I know
the paper used plumed for their colvars, but plumed only works with
constant volume simulations on namd. So, I was wondering if there is a namd
colvar that works similarly. So far I have thought of using distance
colvars to pair residues from each helix, and use those distances to
calculate the rmsd myself. Let me know what you think, any help would be
appreciated.
Thanks in advance,
Ethan
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