From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Sep 09 2020 - 14:55:47 CDT
Hi Ethan, the closest that comes to it in Colvars is the *distancePairs*
function:
https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:cvc_distancePairs
which returns the raw NxM matrix as a flattened vector. You could feed it
into a script function:
https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:colvar_scripted
to do the squared difference from the reference distance matrix. Note that
it would be slow for large groups, because distancePairs was originally
meant to support pairs of few atoms (or copies thereof) such as those used
here:
https://doi.org/10.1371/journal.pcbi.1004368
If you can afford multi-dimensional sampling you could also work with the
tilt and spinAngle functions:
https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:cvc_spinAngle
https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:cvc_tilt
which effectively measure the two relevant angles of relative orientation
(in addition to the COM-COM distance):
https://doi.org/10.1080/00268976.2013.813594
Giacomo
On Wed, Sep 9, 2020 at 3:28 PM Ethan Croitoru <ecroitoru1_at_gmail.com> wrote:
> 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
>
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Research collaborator, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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