Thank you.
I did try addIons2 commands as well, but they take enormous amount of time for a system
of ~140K atoms (the third option I did not explain in my original e-mail), and are not practical for
shell scripts setting multiple MD jobs.
What gives me a pause is that the system at the end of a multi-step equilibration did not lose any atoms
(full system PDB has the same number of atoms, including all the requested ions that are listed in the
topology file, but the BOX_DIMENSIONS section in the PRMTOP lists the same dimensions as the
solvateBox command output. 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?
I will stay with addIonsRand in my scripts, but I would like to understand how this simulation did
not fail?
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
kasprzaw.mail.nih.gov
http://binkley2.ncifcrf.gov/users/kasprzak
________________________________________
From: Parviz Seifpanahi Shabane [sparviz.vt.edu]
Sent: Wednesday, June 13, 2018 3:20 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Net salt ions ouside the solvent box after AddIons
Hi,
"addIons" is usually used for neutralizing a protein, if you want to have
a box with a positive net salt concentration, use "addions2 mol Na+ N
(number of Ion that you need)"
best
On Wed, Jun 13, 2018 at 3:11 PM, Kasprzak, Wojciech (NIH/NCI) [C] <
wojciech.kasprzak.nih.gov> wrote:
> 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.
>
> Commands:
> 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
> kasprzaw.mail.nih.gov
> http://binkley2.ncifcrf.gov/users/kasprzak
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Parviz Seifpanahi
Ph.D. Candidate
Department of Physics
Virginia Tech, Blacksburg, Va 24061
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Received on Wed Jun 13 2018 - 13:00:02 PDT
