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

[petar.zuvela]

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.

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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