[gmx-users] Technqiues for Applying Assymmetric Ion Concentrations?

[Justin Lemkul]

On 6/12/17 10:47 PM, petar.zuvela wrote:
> Isn't it just easier to compute the number of ions ?
> It is basic chem and quite simple.
> N (atoms) = n / mol * Na / mol -1
> n / mol = c / mol dm-3 * V / dm3
> 
> Here V is volume of the box, and c is concentration of either of the ions.
> After computing the number of ions, just add them to the box.
> 
> No need for complicated things like making two water boxes.
> 

It is if you wish to model ion asymmetry across the membrane.

To preserve that asymmetry, one would need semipermeable walls (e.g. flat-bottom 
restraints) that work on the ions but not the water.  That confines the ions to 
their given compartments.  But then, too, the two layers still interact via PBC 
even if ions don't cross the boundary itself.

-Justin

> All the best,
> Petar Zuvela
> 
> 
> 
> Sent from my Samsung Galaxy smartphone.
> 
> -------- Original message --------
> From: Dallas Warren <dallas.warren at monash.edu>
> Date: 6/13/17 10:23 AM (GMT+08:00)
> To: GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Technqiues for Applying Assymmetric Ion Concentrations?
> 
> I'd just make two separate water boxes that are the appropriate size
> to go either side of the bilayer, add required ions to each one, then
> simply join the two coordinate files together with the bilayer by
> simply copy/paste them together. May require adjusting of the
> coordinates by translations before joining.
> 
> BTW, make sure you consider what happens at the other side of the
> water slabs to the bilayer. Are they joined via the PBC?
> Catch ya,
> 
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.warren at monash.edu
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a nail.
> 
> 
> On 8 June 2017 at 11:09, Sanim Rahman <sanimr at mail.usf.edu> wrote:
>> Hello Users,
>>
>> I am planning to do a bilayer simulation with asymmetric ion concentrations
>> using slab boundaries. I am trying to modify the concentration of each
>> ionic species on each side of the bilayer, however, I am struggling to find
>> a technique that will allow me to effectively manipulate the concentrations
>> of each side of the bilayer. Are there any suggestions on how to do this? I
>> would imagine splitting the system in half at the hydrophobic core and then
>> using the genion command for each half would do the trick but I am unaware
>> of any commands that will allow me to split the system as such.
>>
>> The membrane system that I am using is from CHARMM-GUI.
>>
>> I will truly appreciate your input.
>>
>> Regards,
>> Sanim Rahman
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-- 
==================================================

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

==================================================