From: Vijay Vammi (vsvammi_at_iastate.edu)
Date: Thu Jun 14 2012 - 08:09:19 CDT
Multiple copy ligand simulations are performed to find ligand
The method is mentioned in Pi Release From Myosin: A Simulation
Analysis of Possible Pathways, Karplus et al.
Briefly the method requires :
1). multiple copies of ligand at a high temperature compared to the
protein system. The protein system is kept at 300K but the ligand
copies are set at a very high temperature. This can be accomplished by
using Temperature coupling parameters of NAMD. (Please correct me if I
2). The interactions between the ligand and protein are scaled down by
the number of copies and there is no interaction between the ligands.
How to achieve this in NAMD?
Have a good day,
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:39 CST