[gmx-users] Fat-bottom restrain

Mark Abraham mark.j.abraham at gmail.com
Sat Sep 7 16:47:39 CEST 2019


The total potential energy violating the restraints is reported, so you
should see that there is an appropriate contribution there, and probably
plan to stiffen the force constant.


On Fri., 6 Sep. 2019, 17:23 Alex, <alexanderwien2k at gmail.com> wrote:

> 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?
> Regards,
> Alex
> 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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