[gmx-users] Fat-bottom restrain

[Billy Williams-Noonan]

You may want to consider using smart-bottom restraints instead?

Jokes aside, why does it matter if your molecules move into the next
periodic image?

Cheers,
Billy

On Wed., 11 Sep. 2019, 5:03 pm Alex, <alexanderwien2k at gmail.com> wrote:

> Hi,
>
> Any comment, please?
>
> Thank you.
> Alex
>
> On Mon, Sep 9, 2019 at 10:22 PM Alex <alexanderwien2k at gmail.com> wrote:
>
> > Hi Mark,
> >
> > 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
> > (kJ/mol)
> > Coul. recip.                12689.7         12    109.811   -83.8453
> > (kJ/mol)
> > Flat-bottom posres                0          0          0          0
> > (kJ/mol)
> > Potential                -7.29781e+06        540    3208.53   -3702.71
> > (kJ/mol)
> > Kinetic En.              1.20527e+06        8.2    1912.61    -12.144
> > (kJ/mol)
> > Total Energy             -6.09255e+06        540     3942.5   -3714.84
> > (kJ/mol)
> > Conserved En.            -2.97263e+06     890000 1.81911e+06 6.30101e+06
> > (kJ/mol)
> >
> > 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.
> >
> > Thank you,
> > Alex
> >
> >
> >
> > On Sat, Sep 7, 2019 at 10:47 AM Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> >> Hi,
> >>
> >> 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.
> >>
> >> Mark
> >>
> >> 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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