AMBER Archive (2007)

Subject: Re: AMBER: PME and counter ions

From: David A. Case (case_at_scripps.edu)
Date: Wed Dec 19 2007 - 20:41:30 CST

On Thu, Dec 20, 2007, Lars Skjærven wrote:

>
> Section 3.6.3 (amber manual 9) suggests solvating after addIons
> because of potential steric conflicts (waters/ions):
> "If solvent is present, it is ignored in the charge and steric
> calculations, and if an ion has a steric conflict with a solvent
> molecule, the ion is moved to the center of said molecule, and the
> latter is deleted. (To avoid this behavior, solvate after addIons.)".
> Am I misinterpreting something here?

We need to rewrite this: the behavior being "avoided" is not necessarily bad.
I don't think there is any real comparative study, but I would think that
"solvate first, addIons second" is the better way to go.
>
> Looking at the distribution of the counter ions, would you say it is
> "fine" if they are evenly spread around the protein?

Yes.

>
> Heating up to 100K in 20 ps using weak restraints and constant volume.
> Heating up to 300K in 80 ps using weak restraints and constant pressure.
> Equilibration in 300 ps using constant pressure.
> Production runs with constant volume.

What sort of instability do you see? It could be that you should equilibrate
longer with the restraints still in place. But it could also be that there is
some feature of the starting coordinates that will cause "trouble" no matter
what.

...dac

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