free enrgy calculations - an additional information

From: politr_at_huji.ac.il
Date: Wed Jun 04 2008 - 07:07:01 CDT

Dear NAMD experts,
I have to perform free energy calculations of glycerol molecule in
water. 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 and there is also some
additional Alchemical Free Energy Perturbation Calculations. What is the
difference between them and what method should I use for my needs? What
are the input files I need to perform my calculation? 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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