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
>
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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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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat May 09 2020 - 15:30:02 PDT
