Re: [AMBER] addions doubt

From: Bill Ross <>
Date: Wed, 17 May 2017 01:13:54 -0700

Addions after solvation results in each ion replacing a single water.

Adding water after ions results in more waters being removed, since each
ion can overlap multiple waters in the template water box.

More waters being removed results in more vdw voids, leading to more box
shrinkage on equilibration, meaning more uncertainty in choosing initial
box size.


On 5/17/17 12:05 AM, Mary Varughese wrote:
> Hi
> I want to clear one point.
> In normal setting up of a system for simulation.
> We add neutralizing counterions first and then add water solvate. isnt?
> if i want to add extra ions (say for 0.2 M), should i add it before
> or after solvation?
> thanking you
> mary varughese
> _______________________________________________
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Received on Wed May 17 2017 - 01:30:03 PDT
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