Advice on how to perform multiple copy ligand simulation

From: Vijay Vammi (vsvammi_at_iastate.edu)
Date: Thu Jun 14 2012 - 08:09:19 CDT

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Hello all,

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?

Thanks
Have a good day,
Santhosh

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