Thank you to Bill Ross and Matias Machado for the additional comments on the best ion placement!
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
kasprzaw.mail.nih.gov
http://binkley2.ncifcrf.gov/users/kasprzak
________________________________________
From: Bill Ross [ross.cgl.ucsf.edu]
Sent: Thursday, June 14, 2018 2:43 PM
To: amber.ambermd.org
Subject: Re: [AMBER] Net salt ions ouside the solvent box after AddIons
Adding an author's note: the original version of addions just placed
ions in a shell around the solute (with no awareness of a box), due to
hardware limitations at the time.
I think I even used the 1A grid when water is present, first finding the
optimum, then the nearest water, but if I didn't get around to it, it
would make much more sense to just use water O's when present, instead
of a grid, though as stated nowadays better equilibration may make
fine-grain efforts pointless.
Bill
On 6/14/18 11:27 AM, Matias Machado wrote:
> Dear Wojciech,
>
> I guess AddIons (or Addions2) does not take into account PBC (or the box geometry) just the electrostatic potential to place ions, that is way some of the ions may be set "out of the box", which is bad as they may generate clashes though the box images. In addition, those are extremely slow methods for placing ions!
>
> I guess placing ions according to the electrostatic potential is not much used nowadays... a long time ago it was very important because simulations were run for very short times (few ps) and having a good starting reproduction of the ionic environment around the solutes was crucial for the stability of the systems, particularly for polyelectrolytes. Today, equilibrating the system for 100-500 ps is enough to have a good ion distribution. So the starting positions are not a big issue... However if you insists on fixing the initial clustering of some ions then you may try setting a separation to avoid their proximity e.g:
>
> addIonsRand Na+ 120 Cl- 100 5
>
> Notice: I'm assuming the charge of the RNA is -20e and setting a separation distance of 5A among ions
>
> Best,
>
> Matías
>
> ------------------------------------
> PhD.
> Researcher at Biomolecular Simulations Lab.
> Institut Pasteur de Montevideo | Uruguay
> [http://www.pasteur.uy]
> [http://www.sirahff.com]
>
> ----- Mensaje original -----
> De: "Wojciech Kasprzak (NIH/NCI) [C]" <wojciech.kasprzak.nih.gov>
> Para: "david case" <david.case.rutgers.edu>, "AMBER Mailing List" <amber.ambermd.org>
> Enviados: Miércoles, 13 de Junio 2018 17:25:51
> Asunto: Re: [AMBER] Net salt ions ouside the solvent box after AddIons
>
> 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
> kasprzaw.mail.nih.gov
> http://binkley2.ncifcrf.gov/users/kasprzak
> ________________________________________
> From: David A Case [david.case.rutgers.edu]
> 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.)
>
> ....regards...dac
>
>
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