VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu May 12 2022 - 15:23:05 CDT

This is more of a MD question, and also more on the methodology to use
rather than the technical implementation.

For sure, from the existing 10 ns simulation you cannot really say much in
terms of binding free energy. You would need new simulations with methods
capable of computing a potential of mean force. With NAMD, you can use
alchemical methods https://www.ks.uiuc.edu/Research/namd/2.14/ug/ or
geometric ones via the Colvars module:
https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html__;!!DZ3fjg!5ajdPkCuAaXDwofQqnkdipwL0_dk4RngG3-hgkP8KlsiYPQFkTR34Plsy4Xndxsp98aNpPiBNkX5mmYAMaxCzJfb4A$ But
these will require you to investe more computer time and more of your own
time.

I suspect you are in more of a hurry, so I would suggest focusing on
comparing the simulated structures resulting from multiple simulations with
different initial conditions. I know many experimentalists who are very
effective at using MD this way, and it's often more informative than a
free-energy computation done too quickly.

Giacomo

On Thu, May 12, 2022 at 4:01 PM Efthymiou, Christos <
christos.dereschuk.20_at_ucl.ac.uk> wrote:

> Hello,
>
> I am using QwikMD/NAMD to run a 10 ns simulation of a protein-protein
> complex involving two protein chains. I have completed the simulation, and
> now I would like to calculate the free binding energy of the complex. Is
> there a way to calculate the binding energy of a protein complex in VMD? A
> GUI-based method would be preferable.
>