From: Andrew Emerson (a.emerson_at_cineca.it)
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 e-mail: a.emerson_at_cineca.it
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