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.