Re: [AMBER] Net salt ions ouside the solvent box after AddIons

From: Kasprzak, Wojciech (NIH/NCI) [C] <"Kasprzak,>
Date: Wed, 13 Jun 2018 20:25:51 +0000

Dr. Case,

Thank you very much for your reply. I will keep an eye on the updates to ion placement in LEaP.

Best regards, Voytek Kasprzak

Wojciech (Voytek) K. Kasprzak (Contractor)
Bioinformatics Analyst
Basic Science Program
Frederick National Laboratory for Cancer Research
Leidos Biomedical Research, Inc.
Post Office Box B
Frederick, Maryland 21702
Phone: 301-846-5537
From: David A Case []
Sent: Wednesday, June 13, 2018 4:10 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Net salt ions ouside the solvent box after AddIons

On Wed, Jun 13, 2018, Kasprzak, Wojciech (NIH/NCI) [C] wrote:

> Yet ions well outside that water box are clearly visible. So what does PBC
> run do to these atoms? Does it treat them as it would parts of the
> solute drifting outside the primary box
> later in MD?

Yes: that should be what happens.
> I will stay with addIonsRand in my scripts, but I would like to
> understand how this simulation did not fail?

This is wise: we are in the process of changing the way we do simulation
setup, including the way ions are placed. Unfortunately, this may mean
that no one has the real intiative to figure out the problem with the
original AddIons process (which was written 25 years ago or so.)


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