Re: [AMBER] Regarding MD run in vacuum

From: Massimiliano Porrini <m.porrini.iecb.u-bordeaux.fr>
Date: Wed, 3 Apr 2013 18:54:50 +0200

On 3 April 2013 15:53, Jason Swails <jason.swails.gmail.com> wrote:


> Furthermore, you really
> do not have experimental results to compare to that I know of, so you won't
> be able to 'validate' your vacuum simulation against any experimental
> measurements (at least as far as I know -- hopefully someone will fill in
> the blanks if I am mistaken).
>
>
I do not know if I can thoroughly "fill in the blanks", but ion mobility
mass
spectrometry (IM-MS) is an experimental technique able to separate
conformational families of a (let's say) protein in gas phase and through
which one can measure the rotationally averaged collision cross section.

http://en.wikipedia.org/wiki/Ion-mobility_spectrometry

This observable (collision cross section) might be the 'validating' link
between experiments and simulations.

Best,

PS: obviously one has to somewhat prove that the species under
investigation,
passing from solution to gas phase, retain their conformation.




> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
Dr Massimiliano Porrini
Institut Européen de Chimie et Biologie (IECB)
CNRS UMR 5248 Chimie et Biologie des Membranes et des Nano-objets (CBMN)
2, rue Robert Escarpit
33607 Pessac Cedex
FRANCE
Tel   : 33 (0)5 40 00 30 31
Fax : 33 (0)5 40 00 22 00
http://www.iecb.u-bordeaux.fr/
Emails: m.porrini.iecb.u-bordeaux.fr
            M.Porrini.ed.ac.uk
            maxp.iesl.forth.gr
            mozz76.gmail.com
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 03 2013 - 10:00:03 PDT
Custom Search