Re: free energy calculations

From: Eric H. Lee (ericlee_at_ks.uiuc.edu)
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).

-Eric

On Jun 4, 2008, at 5:34 AM, politr_at_huji.ac.il 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
ericlee_at_ks.uiuc.edu

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:49:32 CST