[gmx-users] Calculating Contact Surface Area in one Graph

Justin Lemkul jalemkul at vt.edu
Tue Dec 18 22:28:15 CET 2018

On Tue, Dec 18, 2018 at 2:34 PM Sebastian Muraru <
sebastian.muraru at grabtop.upb.ro> wrote:

> Hi there!
> I am a Masters student trying to figure things out. I am trying to
> calculate the contact surface area between two molecules. I am aware of the
> classic formula, which is CSA = (SASA(complex) - (SASA(molecule1) +
> SASA(molecule2) ) ) divided by 2 and I am aware that we can make graphs for
> each of these terms using gmx sasa. However, if I want to make a CSA graph
> how do I "jump" from knowing how to make the 3x SASA graphs and combine
> them into one graph?
You can get the time series of these values easily in their own files and
write a post-processing script to read the values from files and do the
math. You can use any language you like. It's very simple to do in
languages like Python or Perl.




Justin A. Lemkul, Ph.D.

Assistant Professor

Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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