I am interested in potentially using gromacs to do some calculations
on an C-alpha based elastic network model of the protein that I'm
working on. I'm curious if other users have done similar types of
calculations, and if so, what protocol you used. I realize that there
are a lot of webservers out there that do this calculation, but I
want to be able to use a heterogeneous network of spring constants,
and have a bit more flexibility than many of them allow. Gromacs
seemed like it might be a good option for tackling this problem since
it can calculate the Hessian and generate the normal modes from an
arbitrary force field. it also had a bunch of nice analyses tools
available as well.
Right now I am looking for suggestions on how to explicitly turn off
all non-bonded interactions (the only FF terms are bonded terms). Is
the best option to use energygrp excl? Any other useful suggestions
for using gromacs for this purpose would also be appreciated.
Josh
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