[gmx-users] Electric field or CompEl protocol?

alex rayevsky rayevsky85 at gmail.com
Sun May 20 01:17:13 CEST 2018

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 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 !!

More information about the gromacs.org_gmx-users mailing list