Re: protein unfolding

From: Andrew Emerson (
Date: Thu Jan 21 2010 - 09:45:55 CST

Dear Jose

Since a protein changes it shape drastically during unfolding I
recommend you use NPT rather than NVT, even if you think the box should
  be larger than the unfolded protein. The protein may unfold via a
number of mechanisms and the box should be allowed to change its
dimensions to accommodate them.

best wishes
Andy Emerson

jose correa wrote:
> Dear Leando and Axel
> Thank you for your very fast suggestion. The protein has around 450 residues
> and the water box has 8 A of surface limit. The time of simulation is 25 ns

Dr Andrew Emerson
CINECA (High Performance Systems)
via Magnanelli, 6/3
40033 Casalecchio di Reno (BO)-ITALY

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