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
--
........................................................
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Luca Mollica
Protein Dynamics and Flexibility by NMR
Institut de Biologie Structurale
41 Rue Jules Horowitz
Grenoble
38027
France
E-mail: luca.moll...@ibs.fr (lucamoll...@gmail.com)
Telephone: +33.438783889
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