Re: Multiple copy ligand simulations

From: JC Gumbart (
Date: Thu Jun 14 2012 - 13:42:16 CDT

On Jun 14, 2012, at 1:32 PM, Vijay Vammi wrote:

> 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?
> Thanks
> Have a good day,
> Santhosh

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