Very interesting! Thank you!
> On May 9, 2020, at 7:04 PM, Matias Machado <mmachado.pasteur.edu.uy> wrote:
>
> 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
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>> -----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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>>
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Received on Sat May 09 2020 - 17:30:02 PDT
