Re: free energy calculations

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Jun 04 2008 - 11:52:02 CDT

Hi Regina,
this depends on exactly what type of free energy you want to calculate.
NAMD has tools for calculating free energies for alchemical
transformations (tutorial at
http://www.ks.uiuc.edu/Research/namd/tutorial/fep/AlchemicalFEP-Mar2008.pdf)
or for conformational changes along defined reaction coordinates
(tutorial at
http://www.ks.uiuc.edu/Research/namd/tutorial/abf/ABF-Mar2008.pdf).
Which of these you use depends on what you want to calculate, but both
tutorials should give some good example input files. It's also worth
reading the references in those tutorials to get a wider background on
free energy calculations and see if either of these methods is what
you're after (there are plenty of other ways for calculating free
energies out there).
Best,
Peter

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

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