definitely check out the tutorials on the amber web site if you have not
already.
you'll want to use one of the GB models for the simulation- there are
several, and the pro/con have been fairly well discussed in the literature.
which one is "best" depends on what you are simulating.
the viscosity is controlled with Langevin dynamics (ntt=3 in amber) and
gamma_ln (lower is less). There is a paper a while back from Pande showing
folding rates as a function of viscosity.
I suggest doing the tutorials and coming back with specific questions once
you're up and running.
good luck!
On Tue, Mar 8, 2011 at 3:28 PM, Mahmoud Soliman <mess20.bath.ac.uk> wrote:
>
> Hi guys!
> I need to simulate some big conformational changes in some protein
> structure
> and I came across a paper reporting that continuum solvation with low
> solvent viscosity has proved good ensemble. Do you guys have any previous
> experience with such MD conditions and what keywords I can use in Amber
> script....
> Thanks in advance
> Best wishes
> mahmoud
>
> --
>
> **************************************
>
> Mahmoud E. Soliman
>
> Computational Chemistry & Modeling (PhD)
>
> Department of Chemistry
>
> University of Bath
>
> Bath
>
> BA2 7AY
>
> United Kingdom
>
> [1]http://people.bath.ac.uk/mess20/
>
> [2]http://www.bath.ac.uk/person/812559
>
> Email:
>
> [3]mess20.bath.ac.uk
>
> [4]meelkot.zu.edu.eg
>
> References
>
> 1. http://people.bath.ac.uk/mess20/
> 2. http://www.bath.ac.uk/person/812559
> 3. mailto:mess20.bath.ac.uk
> 4. mailto:meelkot.zu.edu.eg
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 09 2011 - 04:30:05 PST
