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

From: Kasprzak, Wojciech (NIH/NCI) [C] <"Kasprzak,>
Date: Wed, 13 Jun 2018 19:11:55 +0000

 Dear Amber Users,

 I tried 3 LEaP script variants in order to create a solvent box with a positive net salt concentration.
The common commands are:

mol = loadpdb RNA.pdb
addIons mol Na+ 0
solvateBox mol TIP3PBOX 12.0 0.8

At this stage water box with RNA and neutralizing ions inside it is produced.

addIonsRand Na+ 100
addIonsRand Cl- 100
yield the above system with additional ions inside the water box. There appear to be areas
(sub-volumes) of mostly Na+ or Cl- ions, but overall it's fairly well "stirred."

However, using addIons instead of AddIonsRand places quite a few ions well outside
the box, some at distances close to 30A from the RNA. The same equilibration protocol
executed with both systems, but I am not sure how were the ions outside the box
treated in a PME/PBC mix of heating , minimizations and md steps. Could someone
clarify what happens to a system created with all addIons commands.

Thank you in advance, Voytek

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
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Received on Wed Jun 13 2018 - 12:30:01 PDT
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