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.