Re: free energy calculations

From: Eric H. Lee (
Date: Wed Jun 04 2008 - 11:28:13 CDT

If you can define a reasonable reaction coordinate for your system,
you may also want to try out the Adaptive Biasing Force method (also
described in the NAMD documentation).


On Jun 4, 2008, at 5:34 AM, wrote:

> Dear NAMD experts,
> I have to perform free energy calculations. I'm not familiar with it
> at all. I have started with reading NAMD manual and I have some
> questions. I saw that there exist 2 methods for computing the free
> energy: slow growth and MCTI. What is the difference between them?
> What are the input files I need to perform these calculations? Does
> anyone have an example of these input files? As I understand I
> need .conf file and .fep file but I can't understand what exactly
> should be defined in the files.
> Any help will be greatly appreciated.
> Regina

Eric H. Lee
Medical Scholars Program
Theoretical and Computational Biophysics Group, UIUC

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