Re: free energy changes of one subunit

From: Giacomo Fiorin (
Date: Tue Mar 16 2010 - 15:43:52 CDT

Hi Lixia, if you want to extract free energies from the existing 100 ns
trajectory, that's post-processing. It can be done with VMD by plotting
a few variables that best describe the conformational change that you
expect. If you see them going back and forth several times during the
simulation, you can safely compute their histogram and use it as the
probability density of the system.

But if you only see a conformational change once, that's statistically

You should either simulate for much longer, or bias the system to explore
more rapidly the conformational space. In case you're are NAMD 2.7b1 or
later, the collective variables module may be useful to you. Use the
variables that you think are more appropriate, and apply to them one of the
several free energy reconstruction methods, that will drive the system
outside the equilibrium in a controlled way.


---- ----
Giacomo Fiorin
  ICMS - Institute for Computational Molecular Science
    Temple University
    1900 N 12 th Street, Philadelphia, PA 19122
work phone: (+1)-215-204-4216
mobile: (+1)-267-324-7676
---- ----

On Tue, Mar 16, 2010 at 2:39 PM, Lixia Jin Day <> wrote:

> I collected simulation data for a protein complex in water for over 100ns.
> Now I want to focus on one subunit or domain and calculate the free energy
> changes during the 100ns due to the conformational changes in this subunit
> or one of its domains. No reactions will be included, only conformational
> changes. Can any one give me some advices on how to perform this with NAMD?
> Thank you very much!
> Lixia

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