[gmx-users] Computational electrophysiology (compEL) setup issues (Kutzner, Carsten)
francescopetri at hotmail.com
Wed May 29 10:01:23 CEST 2019
Thank Dr Kursten for your reply. I really apprecciate your work on compEL.
>It is even easier to just generate a single bilayer with a channel, and then duplicate the whole system by stacking two copies on top of each other, e.g. with the script found on page www.mpibpc.mpg.de/grubmueller/compel under www.mpibpc.mpg.de/15388676/makeSandwich.tgz
Thanks for the suggestion. I have choosed packmol-memgen because I'm a novel gmx user and I felt more confident with Amber setup (I am performed minimization and equilibration with it and then converted it to Gromacs), but after this training period I will use this script to duplicate the system.
>The .xvg output file also lists the z-position of your split group (=channel) centers over time. Can you check in a molecular viewer whether these make sense? They should be in the middle (regarding z coordinate) of each of the two membranes. This is important, because these z-positions define the compartment boundaries.
I have checked this and the z-position and it is exactly in the middle of each of the two membranes (in details it maps in the channel center).
>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.
>You set -1, so if ions move through the channels, the protocol restores the numbers found at the start of the simulation, which may or may not give you an ionic imbalance and a voltage across the membrane.
You need to put positive numbers there, which add up to the actual number of ions in the simulation, e.g. let?s say you have a total of 20 Cl- and 24 K+ :
iontype0-name = Cl-
iontype0-in-A = 10 # means 10 Cl- in compartment A
iontype0-in-B = 10 # means 10 Cl- in compartment B as well
iontype1-name = K+
iontype1-in-A = 12 # 13 K+ in A
iontype1-in-B = 12 # 11 K+ in B
This will set and keep an imbalance of two elementary charges between the compartments, that will be set at the first time step by exchanging an appropriate number of ions and water between A and B.
This aspect is much more clear now. Thank you again.
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