Hello Florent,
Thanks for the quick response!
Yes, indeed putting counter ions to neutralize the whole system is required
for full PME calculation of electrostatic forces.
This part is fine. I have added counter ions. My systems are neutral.
My question concerns with the effect of *'physiological concentration of
salt'* (say, NaCl) on the configuration of protein.
With or without physiological concentration does the configuration of
protein differs drastically in an MD simulation?
Looking forward to get inputs.
Thanks,
--- Lalit
On Sun, Feb 28, 2010 at 4:16 PM, Barbault Florent <
florent.barbault.univ-paris-diderot.fr> wrote:
> 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 - 16:00:02 PST
