Re: Asymmetric concentration gradient

From: Gumbart, JC (
Date: Tue Aug 24 2021 - 17:34:23 CDT

You can always calculate the concentration according to the equation

# ions *( 55.5 M / # water molecules ) = (ion conc.) M (55.5 M is the concentration of pure water)
* be careful to count water *molecules* and not water *atoms*

As for adding more species of ions, autoionize can do this.


On Aug 24, 2021, at 11:59 AM, Ropon-Palacios G. <<>> wrote:

I understood how to solvate in two parts, now I have a question perhaps a bit silly, but having a membrane and solvate for example {0 60} above the membrane, water molecules are found in the membrane, I eliminate them in a range of z < 26 angstrom, so I do the ionization first with KCl and then with NaCl 10 and 100 mM respectively, checking a little how the autoinize works, I realized that this is based on the volume on the number of molecular water, so if I eliminate molecular water and ionize, am I placing the same concentration ?, because I also checked that it could be an infinite type of solution, where it would not affect much if I add more water, since the concentration of the solute does not vary.

My questions are:
How do I add more than one kind of ions like KCl and NaCl and if when I do this the concentrations that I choose are correct?

From: "Gumbart, JC" <<>>
Date: Tuesday, August 24, 2021 at 12:11 AM
To: "Ropon-Palacios G." <<>>
Cc: NAMD list <<>>
Subject: Re: namd-l: Asymmetric concentration gradient

You can give solvate a minmax to only solvate a region above or below the membrane mid-plane (make sure to give them different segnames for both the water and ions). Then a few lines using psfgen (readpsf ___ pdb ___) will combine them. There’s no script though, but if you play around with the options, you should quickly get a sense of what to do.


On Aug 24, 2021, at 12:10 AM, Ropon-Palacios G. <<>> wrote:

Dear Prof. Gumbart,

My question was on that side, how to do the solvation up and down independently, could you give me an example of the script, to be able to do it please. I find it a bit unfamiliar as this is my first time doing this.

From: "Gumbart, JC" <<>>
Date: Monday, August 23, 2021 at 11:05 PM
To: NAMD list <<>>, "Ropon-Palacios G." <<>>
Subject: Re: namd-l: Asymmetric concentration gradient

Hi Geo,

It’s been a long time since I ran this. But one way I can think of would be to solvate and ionize above and below separately and then combine them with psfgen. I attach an example tclBC script and NAMD input file for running the actual simulation once you’ve built the system.


On Aug 23, 2021, at 10:08 PM, Ropon-Palacios G. <<>> wrote:

Dear users,

I am trying to simulate a membrane protein system where it has a concentration difference on one side as well as the other, similar to the work of Professor JC Gumbart “Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations”

My question is, how do I ionize or how do I place the ions on both sides with a difference in concentration? Could you please share a script to do this?.



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