les + conformational free energy

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Tue May 09 2006 - 08:31:51 CDT

Hi all,

Currently I'm studying a protein (~ 200 aa) and I want to study the
role of phosphorylation on the conformational transitions within a
region of these protein. Up to now I've just used standard MD (I got
around 100 ns of a fully solvated system), but it looks like the
sampling of the region around the phosphorylation site is very poor
(as expected). I've been checking different methods to enhance the
sampling of the PES and I found that NAMD can be used for locally
enhanced sampling simulations. And my question is related to it. Has
anybody had some experience at using LES with NAMD? It will be great
to get some feedback/advise about it.

On the other hand, I also would like to calculate the conformational
free energy induced by phosphorylation. How can I do it with NAMD?

Thank you!



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