Hello,
As far as I know, we put counter ions in MD simulations in order to
neutralize our systems. Indeed, if you use the Particle Mesh Ewald
calculation method to treat electrostatic effect you suppose that the
global charge of your system is zero.
I hope this will help you,
Best regards
Florent Barbault
On Sun, 28 Feb 2010 15:32:05 -0600
Lalit Dubey <dubey.lalit.gmail.com> wrote:
> Dear All,
>
> I got a general question and I desperately need some
>advice/input/expert
> views.
>
> What role the addition or not addition of salt (say, Na+ Cl-), while
>doing
> MD simulations, will play in the configuration of the protein
>configuration
> which is docked in a bilayer?
>
> Any pointers, any paper that deals with the role of salt
>concentration in MD
> simulations would be greatly appreciated.
>
> I have a set of three systems consisting of: protein + lipid bilayer
>+
> counterions + water and run them up to 85ns each. However, I don't
>have
> physiological salt concentration (say, Na+ Cl- ions) in any system.
>I have
> followed the system preparation procedures as given in many papers
>(I can
> quote them easily) and they don't talk about addition of
>physiological salt
> concentration.
>
> Now, I am faced with a question regarding the role of salt in MD
>simulations
> (protein+bilayer systems), especially on the configuration of
>protein?
>
> Is my simulations which doesn't include salt means they are totally
>absurd?
>
> I need any input. Please suggest.
>
> Thanks,
> --- Lalit
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-------------------------------------------------
Dr Florent Barbault
Maitre de conferences / Assistant professor
Universite Paris Diderot
Laboratoire ITODYS
15 rue Jean de Baïf, bâtiment Lavoisier
75013 Paris FRANCE
http://www.itodys.univ-paris7.fr/
tel : (33) 01-57-27-88-50
e-mail : florent.barbault.univ-paris-diderot.fr
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Received on Sun Feb 28 2010 - 14:30:02 PST
