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.
>>
>> --
>> _______________________________________________
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>> 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 - 15:00:02 PDT
