Hi, The usual way to do this is with harmonic bonds (or equivalent distance restraints) from metal to ligand. Those are different from constraints. GROMACS is not built for general rigid-body motion, which is what a fully-constrained tetrahedron would require.
Mark On Sun, 30 Jun 2019 at 20:32, Mahdi Bagherpoor <[email protected]> wrote: > Dear Gromacs users, > > I am trying to simulate a zinc-finger protein in explicit water, *with > CHARMM36 FF*. Unfortunately, I did not find any *tetrahedral zinc force* > field > in Gromacs and therefore I converted the tetrahedral dummy zinc model used > in CHARMM27 FF to the format of Gromacs. The minimization of the system > goes perfect but unfortunately when I start *NVT simulation*, I get this > error: > ------------ > > WARNING 1 [file topol.top, line 57]: > The bond in molecule-type Dummy_chain_X between atoms 2 DZ1 and 3 DZ2 has > an estimated oscillational period of 6.1e-03 ps, which is less than 5 > times the time step of 2.0e-03 ps. > Maybe you forgot to change the constraints mdp option. > ... > Too many warnings (1). > If you are sure all warnings are harmless, use the -maxwarn option. > > ----------- > Here, DZ1 and DZ2 are dummy atoms related to tetrahedral zinc model. *in > mdp file*, I have used *h-bonds* *Lincs* constraint. When I use the > *all-bond* in the mdp file again I get another error that is: > ----------- > > WARNING 1 [file topol.top, line 57]: > There are atoms at both ends of an angle, connected by constraints and > with masses that differ by more than a factor of 13. This means that > there are likely dynamic modes that are only very weakly coupled. To > ensure good equipartitioning, you need to either not use constraints on > all bonds (but, if possible, only on bonds involving hydrogens) or use > integrator = sd or decrease one or more tolerances: > verlet-buffer-tolerance <= 0.0001, LINCS iterations >= 2, LINCS order >= > 4 or SHAKE tolerance <= 1e-05 > .... > Number of degrees of freedom in T-Coupling group Protein_DNA_ZNT is 6936.89 > Number of degrees of freedom in T-Coupling group Water_and_ions is > 179547.11 > .... > > ------------ > Does this error mean that I need to constraint zinc bonds beside h-bonds? > If so, how should I do it? or something wrong in my topology is? *I will > appreciate* if you let me know any idea to fix this problem. > > Cheers, > Mahdi > -- > 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 [email protected]. > -- 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 [email protected].
