[gmx-users] Elastic Network Model

Joshua Adelman jadelman at berkeley.edu
Tue Mar 31 00:23:38 CEST 2009

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.


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