Simulation with denaturants?

From: patrick wintrode (
Date: Sat Apr 29 2006 - 14:00:02 CDT

I'm planning to run MD simulations of a protein in the presence of 1M GuHCl (we've already mostly finished the simulations in water). I know that parameters for GuHCl exist, because I recall that the Karplus group published some unfolding simulations with it.

I was wondering: does anyone know of a script for placing the denaturant molecules in the water box? Maybe a script for some similar problem that I could modify?

Also, we can use Urea instead. Do you think that the high ionic strength resulting from 1M GuHCl will cause particular problems that would make Urea preferable?


Patrick L. Wintrode
Assistant Professor
Dept. of Physiology & Biophysics
Case Western Reserve University
Cleveland, Ohio 44106

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