[gmx-users] Fat-bottom restrain
alexanderwien2k at gmail.com
Tue Sep 10 04:22:54 CEST 2019
Thank you for your response.
Here are the part of options that gmx energy gives me out:
9 Coulomb-(SR) 10 Coul.-recip.
11 Flat-bottom-posres 12 Potential
13 Kinetic-En. 14 Total-Energy 15 Conserved-En
Energy Average Err.Est. RMSD Tot-Drift
Coulomb (SR) -8.4629e+06 150 5041.75 -840.379
Coul. recip. 12689.7 12 109.811 -83.8453
Flat-bottom posres 0 0 0 0
Potential -7.29781e+06 540 3208.53 -3702.71
Kinetic En. 1.20527e+06 8.2 1912.61 -12.144
Total Energy -6.09255e+06 540 3942.5 -3714.84
Conserved En. -2.97263e+06 890000 1.81911e+06 6.30101e+06
As can be seen above the Flat-bottom posres energy is just zero during the
simulation; and even stiffening the force constant from 4184 KJ/(mol. nm^2)
to 4184000 KJ/(mol. nm^2) doesn't change anythings and the Flat-bottom
posres energy would remain absolutely zero!
I rechecked everything and I don't see any problem with the way I have set
the flat-bottom restrain.
Any comment would be highly appreciated.
On Sat, Sep 7, 2019 at 10:47 AM Mark Abraham <mark.j.abraham at gmail.com>
> 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
> > 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
> > too low to keep the molecules inside the smaller box! I wonder if you
> > 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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