From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Tue Oct 03 2017 - 12:45:09 CDT
in my current umbrella sampling simulations for ion permeation through the
channel I see ion shifting off the center line (where it supposed to be
located) near the entrance or exit of the pore (no shift in the windows
inside the pore). It seems to move to the nearest strong residue and stay
there throughout simulation without returning back to the specified centre.
The ion can move 2-3 A to the side over the first 0.5-1 ns and linger there
for the rest of the simulation. I use distance colvar for this simulation.
I would expect that for umbrella sampling the ion should not shift that far
from a specified location (and I haven't seen this in my previous US
simulations on a similar system). What would be the reason for this to
happen in US simulations?
I want to try using distanceXY colvar to restrain this movement. Is is
applicable in this case, in addition to distance colvar (i.e., not
distanceZ, but distance)? Do I have to have a separate input file for
distanceXY colvar or can I add it into the same *.in file as I have for
Thanks in advance, I appreciate your advice.
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