[gmx-users] Pull code - two reaction coordinates

Dariush Mohammadyani d.mohammadyani at gmail.com
Mon Nov 14 17:03:48 CET 2016


I have a question about the pull code and the umbrella sampling using gmx.
I would like to calculate the free energy of interactions of two proteins,
but I am interested in defining two sites on these proteins, which their
distances are my coordinates. I assume pulling two sites of a protein
should be problematic. I am wondering to know how pull code will work to
pull only parts of two proteins? To make it more clear, proteins A has site
1 and 2, and protein B has site 3 and 4. The first coordinates will be the
distance of sites 1 and 3 and the second one will be the distance of sites
2 and 4. This approach would give us a better 2D PMF plot to find out a
more accurate binding orientation.


Dariush Mohammadyani, Ph.D.
Postdoctoral Researcher
Department of Biophysics
Johns Hopkins University
Baltimore, USA

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