Re: protein unfolding

From: jose correa (
Date: Thu Jan 21 2010 - 09:55:14 CST

Dear Andy
I start with NTP (150 ps) and then NTV, but the protein was unfolded
inmediatelly with NTV. I ask it to a colleage who sugest me that, it is
preferible start and mantain NTV due to with NTP, the water are boiling and
the protein-water contats dissapear, then, it yield data not reliable. But,
if you think or have a paper that report this condition (NTP), I can try.
Best wishes and thank you
ESM-IPN, México
2010/1/21 Andrew Emerson <>

> 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:

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