Multiple copy ligand simulations

From: Vijay Vammi (
Date: Thu Jun 14 2012 - 13:32:43 CDT

Hello all,

Sorry if this is a repetition but the first mail did not go through.

Multiple copy ligand simulations are performed to find ligand
migration pathways.
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
am wrong)
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,

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