[gmx-users] asking help for simulation of protein in 8M urea

[Luca Mollica]

On 05/20/2010 09:05 AM, caty hacker wrote:
> Dear all,
>             I want to a protein simulation in 8M urea. Can anyone 
> suggest me any introductory tutorial on that. Thank you in advance.

I think a "tutorial" is useless for such a simulation. Papers are the 
best reference depending on what you want to simulate
and on what you want to "see": if you are trying to simulate the 
unfolding there are several publications that discuss the major issues 
of the field, i.e.

a. which ff and/or urea topology to use
b. which computational technique (REMD, MD, MetaMD ...) to use

So ... what's your goal ? :)
At the moment I am too working on some systems that require the usage of 
urea and doing a bit of set up for AMBER FF, whereas in the past I have 
used a
topology for the last GROMOS FF.

Cheers

Luca


-- 

........................................................

--



Luca Mollica
Protein Dynamics and Flexibility by NMR
Institut de Biologie Structurale
41 Rue Jules Horowitz
Grenoble
38027
France

E-mail: luca.mollica at ibs.fr (lucamollica at gmail.com)

Telephone: +33.438783889


--


Elwood: It's 106 miles to Chicago, we got a full tank of gas, half a pack of cigarettes, it's dark, and we're wearing sunglasses.
Jake: Hit it.

(The Blues Brothers)