From: felmerino_at_uchile.cl
Date: Tue Mar 16 2010 - 15:29:17 CDT
Hi Lixia,
You cannot calculate free energy changes through a conformational change from a
conventional molecular dynamics. What you need is to use some other technique
such as ABF, metadynamics, etc, but it would depend on your system and the
magnitude of the change.
best
felipe
> 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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