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

Tsjerk Wassenaar tsjerkw at gmail.com
Thu May 20 09:54:38 CEST 2010

Hi Caty,

In addition to Luca's comments, also consider what you mean with 8M.
Molarity is defined as mole per liter, but the addition of urea may
have an effect on the volume, such that adding a volume x urea to a
volume y water does not yield a volume x+y. Especially with such high
concentrations you might be better off with molalities (mole/kg).
Then you probably want to first generate a box of urea in water by
adding a adding a box of water to a box of urea and letting it diffuse
(at a high temperature). But only after you figured out the answers to
Luca's questions :)



On Thu, May 20, 2010 at 9:32 AM, Luca Mollica <luca.mollica at ibs.fr> wrote:
> 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
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands

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