[gmx-users] Fat-bottom restrain

Alex alexanderwien2k at gmail.com
Fri Sep 13 16:32:19 CEST 2019


Hi Mark,

I am using Gromacs v.2018.x and as I tested it is not the matter of using
GPU or CPU.
The issue was from my side where by mistake I had put the wall (in all
posre.x,y,z.itp) exactly on the outer box borders so that my inner box and
outer box were fully identical,
so the molecules had no limitation and wherever of the simulation box they
could go, that is why the gmx energy shows the "Flat-bottom posres" portion
but it was absolutely zero.

However, my question now is; do I have flat-bottom restrains in these
simulation or not? e.g. If I want to report these simulations somewhere
should I mention that I have used (I haven't used) flat-bottom restrains in
these simulation?

Thank you
Alex

On Wed, Sep 11, 2019 at 8:01 PM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> It's certainly conceivable that such restraints are ineffective in some run
> modes. However, "on the GPU" describes a range of scenarios. If you're
> running with 2019.x, does adding -bonded cpu to the mdrun command line
> restore the functionality?
>
> Otherwise, please try the "working CPU" run on a GPU resource and vice
> versa to see what we learn.
>
> Mark
>
> On Wed, 11 Sep 2019 at 23:21, Alex <alexanderwien2k at gmail.com> wrote:
>
> > Thanks Billy,
> >
> > > If the flat bottom restraint energy is zero, then that means that the
> > > restraints aren't being applied, or your predefined distance is not
> being
> > > exceeded.  I doubt you would get binary zero values if it was the
> second
> > > option, so something is probably wrong with your syntax or your
> inclusion
> > > of the restraints
> >
> > As far as I have inspected everything is fine with the syntax and
> > application of the restraints. Using similar way works fine in another
> > system. The only difference is that one (not working one) runs on GPU and
> > the other one (the working one) runs on CPU, and I am not sure if that
> > plays any role and if the flat-bottom restrain doesn't work on GPU!
> >
> > >
> > > Cheers,
> > > Billy
> > >
> > > On Wed., 11 Sep. 2019, 5:20 pm Billy Williams-Noonan, <
> > > billy.williams-noonan at monash.edu> wrote:
> > >
> > > You may want to consider using smart-bottom restraints instead?
> > I haven't hear the smart-bottom one, would you please explain more? or
> > address me to a reference?
> > >
> > > Jokes aside, why does it matter if your molecules move into the next
> > > periodic image?
> > Just to avoid percolation across the period box.
> > >
> > > Cheers,
> > > Billy
> > Thank you,
> > Alex
> >
> > On Wed, Sep 11, 2019 at 3:02 AM 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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