[gmx-users] Electric field or CompEl protocol?

[alex rayevsky]

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
membrane.
These two of 20 articles I've found on the theme befor wrote in gmx
society:
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://www.mail-archive.com/search?l=gromacs.org_gmx-users@maillist.sys.kth.se&q=from:%22Alex%22>
Sat, 19 May 2018 17:35:15 -0700
<https://www.mail-archive.com/search?l=gromacs.org_gmx-users@maillist.sys.kth.se&q=date:20180519>

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
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.

Alex


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
pagehttp://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 !!





*Nemo me impune lacessit*