[gmx-users] Can't observe ion separation under the influence of electric field

[David van der Spoel]

Den 2020-02-12 kl. 23:07, skrev Live King:
> Dear all,
> 
> I am running a simple test case with a lipid bilayer (DMPC), water, and
> ions (150mM KCL) under the influence of a constant electric field ( 300mV,
> 500mV, and 700mV). *I expected positive and negative ions to separate in
> the presence of an external electric field*. However, I am not observing
> such behavior despite running the all-atom simulation for 400ns in any
> case. I am using gromacs 2018.2, my mdp file is standard charmm-gui
> production with electric field option.
> 
> for example 500mV electric field in Z-direction :
> electric-field-z =      0.060  0     0     0 ; *500**mv  = 8.25nm* 0.060 =
> 500 mV *
> 
> 
> Are there any settings to run the electric field simulation that I miss?
> Any help will be greatly appreciated.
> 
Did you make density plots to check?

Do you get an output field.xvg that prints the field strength? It may be 
optional though.

The force on the atoms will be quite small still compared to interatomic 
forces therefore the effect may be limited. F = q E (convert to right 
units). In GROMACS MD units a typical interatomic force is ~ 1000 
kJ/mol/nm^2.

> 
> Thank you,
> 


-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se