[gmx-users] Fat-bottom restrain
Mark Abraham
mark.j.abraham at gmail.com
Thu Sep 12 02:01:15 CEST 2019
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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