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, <alexanderwie...@gmail.com> wrote: > Hi, > > Any comment, please? > > Thank you. > Alex > > On Mon, Sep 9, 2019 at 10:22 PM Alex <alexanderwie...@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.abra...@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, <alexanderwie...@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. > >> > -- > >> > Gromacs Users mailing list > >> > > >> > * Please search the archive at > >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> > posting! > >> > > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > > >> > * For (un)subscribe requests visit > >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> > send a mail to gmx-users-requ...@gromacs.org. > >> > > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.