AMBER Archive (2009)

Subject: Re: [AMBER] sodium ions before or after solvation makes a difference

• Previous message: FyD: "RE: [AMBER] Comparison of the CHARMM and AMBER parameters for alkane"
• Maybe in reply to: Naser Alijabbari: "[AMBER] sodium ions before or after solvation makes a difference"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

> For an 8 angstrom of water shell around a protein

10A would be more normal, with an 8A cutoff.

> 1) When Na+ is added before solvation 3686 H2O molecules are added (Box X =
> 51.627 Box Y = 58.077 Box Z = 56.547)
>2) When Na+ is added after solvation there are 3496 H2O molecules (which
>makes sense) (Box X = 51.627 Box Y = 56.610 Box Z = 56.547)
>What happens in case 1?

When Na+ is added before solvation, the solvation box is bigger
because the clearance is measured from the Na+. When Na+ is added
after solvation, it replaces waters in the smaller box.

Bill

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

• Previous message: FyD: "RE: [AMBER] Comparison of the CHARMM and AMBER parameters for alkane"
• Maybe in reply to: Naser Alijabbari: "[AMBER] sodium ions before or after solvation makes a difference"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]