[gmx-users] Fat-bottom restrain

[Alex]

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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