[gmx-users] Ion self-interaction energy?

[Rodney Versace Babilonia]

Hi all,

I am trying to simulate the effusion process of water through hole in a very thin film. The film is partitioning the water box, I wish to count the numbers of waters before and after the simulation in each compartment, but I am afraid that the use of periodic boundary conditions will make waters from one side going to the other side through the boundaries and that affect my counting, in case I turn off the PBC, what kind of electrostatic treatment should I use?

Thanks

-Rod 
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Leandro Bortot <leandro.obt at gmail.com>
Sent: Tuesday, August 4, 2015 11:36 AM
To: gmx-users
Subject: Re: [gmx-users] Ion self-interaction energy?

Thank you, Justin. I'll double check for such things in the next analyzes.


On Tue, Aug 4, 2015 at 12:24 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/3/15 10:21 PM, Leandro Bortot wrote:
>
>> Dear users,
>>
>>       I simulated system consisting of a protein complexing a single
>> calcium
>> cation. I used explicit water and ions (Na+ and Cl-) in the solution to
>> neutralize the charge and mimic ionic strenght effects.
>>
>>       I was investigating some interactions and found that if I select the
>> energy term "Coul-SR:CA-CA" with g_energy I got a constant value of
>> -979.327 kJ/mol. I checked and the "CA" group indeed correspond to the
>> single Ca2+ in the simulation.
>>      What is the meaning of this "self-interaction" energy? How should I
>> interpret it?
>>
>>
> As buggy or incorrect.  An atom should have no interaction with itself.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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