[gmx-users] Electric field or CompEl protocol?
nedomacho at gmail.com
Sun May 20 09:55:14 CEST 2018
I think CompEl is described in the manual, the options for it are here:
I've never used it, so I can't suggest anything, but you can ask on this
board for specific mdp examples.
The way CompEl works is conceptually simple: it maintains a
transmembrane ionic concentration gradient by swapping ions across the
periodic boundary. The result is that on average you get a voltage of
(kT/q)log(c_above/c_below) across the system. In reality, you get noisy
results (see Fig. 3 (b) in http://www.mpibpc.mpg.de/grubmueller/compel
). On the other hand, if you have long simulated times, you can still
get clean data.
The problem with using a constant field is that it is only physical for
a system with a nearly constant dielectric throughout. I am guessing
that is not your case and you have water (epsilon ~80) and a lipid
membrane (eps ~ 5?). If there was a real voltage across such a box, it
would almost entirely drop across the membrane (i.e. high field across
membrane and low field elsewhere). This is why I prefer to use fields
that are as low as computationally possible.
I would try CompEl at least out of curiosity. In principle, it is a
solid idea, but I think this algorithm is clunky and how it agrees with
PBC is unclear to me. If you get clean and reasonable data, please let
everyone know! :)
On 5/20/2018 1:16 AM, alex rayevsky wrote:
> Dear Alex!
> Yes, I thought about all Your reflections and I'm also not sure that CompEl
> is well parameterzied for a non-specialist like me and the electric field
> is more intuitive for me. However, when I saw the dimension 'V/nm' for the
> first time, I thought that something must depend on the length of the axis
> of application (in my case it is about 12 nm) or the thickness of the
> These two of 20 articles I've found on the theme befor wrote in gmx
> Structural and Functional Effect of an Oscillating Electric Field on the
> Dopamine-D3 Receptor: A Molecular Dynamics Simulation Study. ( DOI:
> 10.1371/journal.pone.0166412 ) and Molecular dynamics of ion transport
> through the open conformation of a bacterial voltage-gated sodium channel.
> ( https://doi.org/10.1073/pnas.1214667110). ANd this method works fine, in
> general, they've got what they wanted.
> But there is no full description of parameterization. what can You say?
> Thank You
> At the same time compel method is very popular too, here is another mention
> of CompEl - http://dx.doi.org/10.1016/j.bpj.2017.02.016
> Alex <https://email@example.com&q=from:%22Alex%22>
> Sat, 19 May 2018 17:35:15 -0700
> 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 sothat you do not slow down your simulation too
> 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
> 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
> 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
> pagehttp://www.mpibpc.mpg.de/grubmueller/compel duplicates a gromacs
> 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 !!
> *Nemo me impune lacessit*
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