[gmx-users] Computational electrophysiology (compEL) setup issues (Kutzner, Carsten)

Kutzner, Carsten ckutzne at gwdg.de
Wed May 29 11:25:10 CEST 2019

Dear Francesco,

> On 29. May 2019, at 10:01, Francesco Petrizzelli <francescopetri at hotmail.com> wrote:
>> A cyl0-r (and cyl1-r) of 0.7 nm is too small for a pore radius of 3 A to reliably track the ions, some might sneak through your channel without being recorded in the cylinder. Rather choose this value a bit too large than too small. It should be *at least* half of the pore radius.
> Regarding this aspect I'm not sure I got what you mean. The pore radius is 3 A, and I set up the cyl0-radius of 0.7 nm, which should correspond to about 7 A. You said it should be half of the pore radius and I am confused about this. If this can help, the structure that I am using to test this tecnique (I am planning to perform a large number of simulation on different channels) is 5va1 (KCNH2). Actually, I recalculated the pore radius and it is larger than 3 A because I have only considered the selectivity filter.
Sorry my bad! If the pore radius is 0.3 nm, then 0.7 nm cylinder radius is sufficient.
The idea is to select the cylinder dimensions such that each ion that 
permeates through the channel *has* to go through the cylinder. This is only for counting
how many ions permeate through channel A versus channel B. The CompEL ion/water swapping
protocol will work independent of the permeations counting as to perform the swaps
it is only important how many ions of each type are in each compartment.


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