From: Axel Kohlmeyer (
Date: Mon Apr 22 2013 - 03:35:20 CDT

On Mon, Apr 22, 2013 at 4:40 AM, yp sun <> wrote:
> Dear VMD users,
> I want to calculation the free energy of a peptide binding to a protein and
> the energy contribution of individual residues of the peptide. I have
> finished namd simulation, could anyone help me with that? where can I find
> the scripts to realize it?

there are a number of problems with your inquiry:

- to compute free energies, you usually will need to run (multiple)
additional simulation(s)
- before even doing that, you have to choose a suitable method for
your specific problem
- you did a simulation of what?
- you ask to compute a _free_ energy (or rather a free energy
_difference_), which includes an entropy term. how do you propose to
map the entropy component to individual residues? (and what about

it looks to me that you should first inform yourself a bit more about
the statistical mechanics foundations of free energy calculations,
then research which of the multiple available approaches is best
suited for your needs and what kind of analysis is (at all) possible
and only then do the necessary simulations. how to analyze them should
be evident by then.


> Best regards,
> Yeping Sun
> CAS Key Laboratory of Pathogenic Microbiology & Immunology
> NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.