From: Ryan Woltz (
Date: Fri Oct 22 2021 - 15:05:58 CDT

Dear Community,

       From other posts I know this problem has been addressed a few times
for the protein, but when I solve the protein issue I find other problems.
I have a membrane embedded channel and I'd like to look at how the protein
interacts with different lipids. I have 2 systems 1) POPC only 2) 90%
POPC/10% PIP2 (SAPI24) in the lower leaflet. Very basically I want to track
various lipid distances/packing/velocities around specific amino acids. I
have two problems.

1) lipids that I want to measure distances with are jumping to the opposite
side of the box (not quite another box ~95-101 angs in a 135 ang box)

2) In half of the simulations I also have peptide jumping (solved with
commands below) but when I correct for this using the pbc commands the
water freely jumps to other boxes leaving only a couple waters in the
original box by the end of the simulation. This is a problem as a big part
of the simulation is water interaction with the Selectivity filter region
of the channel. Also still problems with lipid jumping from problem 1.

I've asked around some labs and everyone is aware of the problem but nobody
has a concrete solution beyond "try different variations until it works". I
was wondering if anyone has a script or tips on how to adjust my commands
to get everything into the same box.

restypes that are jumping.
water - TIP3

Current commands used (I use -bondlist to bond everything from what I


   pbc join fragment –bondlist –now

   pbc wrap –centersel protein –center com –compound fragment –all

   pbc unwrap

Thank you for any help you can give,

Ryan Woltz