[gmx-users] Fat-bottom restrain

Alex alexanderwien2k at gmail.com
Fri Sep 6 17:22:45 CEST 2019

Dear all,
Using the flat-bottom (K=4184 KJ/(mol. nm^2)) restrain I tried to have a
smaller cubic box as semi-preamble walls inside a bigger cubic box so that
all molecules except water would stay inside the smaller box during the
simulation, however, the wall doesn't work and the molecules are also out
of the smaller box in several replica's simulations each with 100 ns.
The only reason I can imagine is that the K=4184 KJ/(mol. nm^2 is probably
too low to keep the molecules inside the smaller box! I wonder if you know
any other potential reason? how can I find out the reason?

P.S. I am sure that I am using the flat-bottom restrain correctly as the
same approach worked for some other systems of mine previously.

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