[gmx-users] Electric field or CompEl protocol?

Alex nedomacho at gmail.com
Sun May 20 02:34:27 CEST 2018

It's more of a philosophical question in, unfortunately. I don't use 
CompEl, because I believe it is conceptually clunky, but that's a matter 
of opinion that could turn into discussion beyond the scope of your 
question. I don't study biomolecules, so I can get away with applying 
direct fields. For biomolecules, however, I do suggest at least looking 
into CompEl and how it works, and then choosing appropriate setup so 
that you do not slow down your simulation too much.

That said, 0.4 V/nm does not really correspond to 40 mV in any way. The 
best "fake" guess is that the voltage drop across the entire box is its 
height, times the value of E-z. It is fake, because your field has 
nothing to do with the solution of the Poisson's equation, or the box 
height. The consequences of this field do, but the field itself doesn't, 
if that makes sense. One other point to be made: water's dielectric 
breakdown threshold is around 100 MV/m = 0.1 V/nm. Noone in the 
community that publishes in Biophysical Journal seems to care about it, 
but huge simulated fields can be incompatible with what's being studied.

My response probably doesn't help much, but this is the situation with 
all MD software that relies on Ewald summation.


On 5/19/2018 5:16 PM, alex rayevsky wrote:
> Dear all,
> Which protocol, Electric field section or the CompEl, I should use in the
> situtation:
> 1. I built an ion channel by homology, prepared a bilayer membrane, embeded
> my protein and run a simulation to relax the system (100 ns)
> 2. my channel was closed all the time.
> 3. I want to run four parallel simmulations, starting from the relaxed
> state:
> a) system under the effect of -80 mV and under +40 mV - the second one
> should cause a pore opening;
> b) both previous variants with a ligand in the pore;
> The voltage sensitive domain of the Nav channel should respond to the
> electric stimuli, that is why I thought it is reasonable to apply it to Z
> direction and assign electric-field-z = 0.4 0 0 0 for +40mV state, for
> example. other parameters should stay intact, I think, because I don't know
> if they should be changed...
> at the same time I've read several different works when CompEl was
> implemented to the membrane-channel systems. The end of the page
> http://www.mpibpc.mpg.de/grubmueller/compel duplicates a gromacs manual,
> however I didn't find any mention of a voltage handling and what exactly
> I'll obtain at the end....
> Which method is more approrpiate for my task?
> Thank You !!

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