The reasoning behind addions2 is interesting. However, when used to place additional solute ions around a DNA oligomer, the placement is not consistent with the ion distribution at equilibrium. Invariably addions2 places all the ions on one side of the oligomer in a rather tight configuration of ions whereas in the equilibrated structure, the ions are distributed around the oligomer and the rest of the box.
That, at least, has been my experience. Perhaps the calculation of electrostatic potential in the code needs to be inspected to determine why this bias exists. It makes no sense to place Na+ ions on one side of a DNA oligomer when the negative charges on the DNA oligomer are distributed around the double helix.
Jim
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-----Original Message-----
From: Matias Machado <mmachado.pasteur.edu.uy>
Sent: Saturday, May 09, 2020 7:04 PM
To: AMBER Mailing List <amber.ambermd.org>
Cc: James Kress <jimkress_58.kressworks.org>
Subject: Re: [AMBER] addions
In brief, addIonsRand randomly replaces water molecules by ions, hence the obtained distribution is different every time it is generated and have no a prior relationship with the distribution at equilibrium in the presence of the solute.
On the contrary, addIons(2) places the ions at regions of high positive/negative electrostatic potential, hence the distribution is unique for each system and is expected to be close to the distribution at equilibrium. The reason for observing that "addions2 yields a very localized collection of ion" it's just a consequence of following the electrostatic potential, which is high near the solute... however such perception depends on the amount of ions that are added to the simulation box.
Other important differences like PBC are discussed in this thread [
http://archive.ambermd.org/201806/0163.html]
Best,
Matias
----- Mensaje original -----
De: "Robert Molt" <rwmolt07.gmail.com>
Para: "James Kress" <jimkress_58.kressworks.org>, amber.ambermd.org
Enviados: Sábado, 9 de Mayo 2020 19:13:44
Asunto: Re: [AMBER] addions
Is there a fundamental reason why, independent of empirical observation? How do the algorithms differ in this regard? The manual simply says one replaces solvent particles whereas the other does not.
> On May 9, 2020, at 5:56 PM, James Kress <jimkress_58.kressworks.org> wrote:
>
> In my experience, addions2 yields a very localized collection of ions.
> Addionsrand does a much better job of distributing the ions throughout
> the box.
>
> Jim
>
> James Kress Ph.D., President
> The KressWorksR Institute
> An IRS Approved 501 (c)(3) Charitable, Nonprofit Corporation
> "ENGINEERING THE CURE" C
> (248) 573-5499
>
> Learn More and Donate At:
> Website: http://www.kressworks.org
> Facebook: https://www.facebook.com/KressWorks.Institute/
>
> Confidentiality Notice | This e-mail message, including any
> attachments, is for the sole use of the intended recipient(s) and may
> contain confidential or proprietary information. Any unauthorized
> review, use, disclosure or distribution is prohibited. If you are not
> the intended recipient, immediately contact the sender by reply e-mail
> and destroy all copies of the original message.
>
> -----Original Message-----
> From: Robert Molt <rwmolt07.gmail.com>
> Sent: Saturday, May 09, 2020 5:35 PM
> To: amber.ambermd.org
> Subject: Re: [AMBER] addions
>
> Can commentary be offered why one should use addionsrand as opposed to
> addions2?
>
>> On May 6, 2020, at 12:17 PM, Christina Bergonzo <cbergonzo.gmail.com>
> wrote:
>>
>> Hello,
>>
>> You can use the same addions command to add the number of ions that
>> make up your salt composition and concentration (I recommend using
> addionsrand).
>> In the following example I add Cl- ions to neutralize the charge in
>> the first command, and then add the desired number of ions to make up
>> the right salt concentration in the second command (FYI this is a
>> large system and I'm running with 1M salt).
>>
>> Example:
>> addionsrand mol Cl- 0
>> addionsrand mol Na+ 2448 Cl- 2448
>>
>> You can reference the manual for additional guidance.
>>
>> -Christina
>>
>>
>> On Wed, May 6, 2020 at 11:55 AM Jisha B <jisha.b.k0511.gmail.com> wrote:
>>
>>> Dear all,
>>> I have this system where I need to add the counterions of Na+ and
>>> the salt of 1M NaCl according to a protocol.
>>>
>>> I am aware of how to add Na+ using "addions cc Na+ 0" command in
>>> tleap. But I have no idea how to add the salt part. How to do that?
>>> Could someone guide me on this? I am a beginner.
>>>
>>> --
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>> --
>> -----------------------------------------------------------------
>> Christina Bergonzo
>> Research Chemist
>> Biomolecular Measurement Division, MML, NIST
>> -----------------------------------------------------------------
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Received on Sat May 09 2020 - 20:00:03 PDT
