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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Received on Sun Feb 28 2010 - 14:00:03 PST
