From: Uday Chippada (chippada_at_eden.rutgers.edu)
Date: Mon Oct 25 2004 - 16:16:46 CDT
I have a simple question. When we write the configuration file for the SMD simulation, where do we specify the hydrogen cut off distance.
I am doing a simulation for 1QSU by fixing one end and pulling on the other end, and I am interested in counting the number of hydrogen bonds that break during the simulation. But I am not sure what hydrogen cut off distance and cut off angle I need to specify while visualizing in VMD.
Is there an inbuilt cut off distance and angle that NAMD uses while performing the simulation?
Any help would be appreciated.
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