There are any gb models, as well as many sets of intrinsic born radii that
can be used with them. I wouldn't rule them all out.
Regarding explicit solvent, if you use constant volume you can go quite
high. Be aware that you might need smaller time steps to keep integration
stable. Also, you can get non Arrhrenius effects where the search become
more difficult at higher T. You will also have to decide on and validate
the annealing schedule.
On Nov 21, 2013 5:24 AM, "Thomas Evangelidis" <tevang3.gmail.com> wrote:
> Dear list,
>
> What is the maximum temperature one could use in a simulated annealing
> protocol with an explicit solvent model (e.g. SPC/E)? I have a peptide with
> a lot of NOE restraints and J-couplings and I would like to create native
> like conformations. The reason I prefer the explicit solvation is because I
> had bad experience with implicit solvent simulations of intrinsically
> disordered peptides. I had initiated a relevant thread in the past where I
> stated that at the end all the peptides adopted a helical conformation
> which was in disagreement with the NMR and CD spectra.
>
> thanks,
> Thomas
>
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> GREECE
>
> email: tevang.pharm.uoa.gr
>
> tevang3.gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Thu Nov 21 2013 - 04:00:03 PST
