Re: [AMBER] about ions

From: Jason Swails <>
Date: Fri, 24 Aug 2012 22:57:04 -0400

On Fri, Aug 24, 2012 at 8:44 PM, Carlos Romero <>wrote:

> Dear David
> Thanks a lot for your answer.
> >From question about ions and proteins. I try to simulate complex thombin -
> par1 interacting with MgSO4 at different concentrations. Do you recommend I
> do simulations with explicit solvent?

It depends on what you're trying to learn. If you just want the average
electrostatic screening effects of the ions, then you can probably get away
with implicit solvent (it's important to know the limitations of GB,

If you want to look at specific ion-protein interactions that cannot be
attributed to simple screening, then you're stuck with explicit.

In both cases, however, it's very difficult to probe the difference between
0.005 M, 0.025 M, and 0.05 M. Dave has already mentioned the difficulties
involved with differences at such low ionic strength. For explicit
solvent, the size of the periodic box would have to be too large in order
to simulate such low concentrations.

Of course it's always a good idea to look through the existing literature
to see what others have done in this regard.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Fri Aug 24 2012 - 20:00:03 PDT
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