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.
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:38:56 CST