How do you use EXTRABONDS in NAMD?

Aishwary Shivgan @Aishwary_Shivgan

12 December 2014 1 10K Report

I want to do a simulation with restraints using Extrabonds. Does anybody know how to do it?

Suresh Gorle

add these lines in the NAMD configuration file.

extrabonds on

extrabondsfile bonds.txt

the file "bonds.txt" should contain the details of your restraints. Please have a look at this.

http://www.ks.uiuc.edu/Research/namd/2.7/ug/node26.html

Hope this helps

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