From: Shirley Hui (shirleyhui_at_alumni.uwaterloo.ca)
Date: Thu Apr 22 2004 - 13:02:07 CDT
I was wondering if anyone could clarify some things for me.
NAMD's Free Energy Calculator was meant to calculate the free energy change between various perturbations of a molecule (the perturbations would be constrained).
Does anyone know if it is possible to give NAMD two conformations of the same molecule and then calculate the free energy change between the two?? Basically I am perturbing a molecule myself and then I want to know the free energy change between the original conformation of the molecule and the perturbation I made. If not NAMD are there any other software that can do this?? If not, I guess I will have to implement my own and I know this is not a trivial task.
Thanks for any insight, the examples on the web page on NAMD's Free Energy Calculator are a bit too in depth or detailed for me at the moment to fully understand.
http://www.ks.uiuc.edu/Research/namd/current/ug/node33.html
thanks,
shirley
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