I do not see much connection between bond constraints and treatment of electrostatics beyond the cut-off distance.
There is also an "epsilon_r" keyword. I would investigate what exactly it means and whether it is used in the reaction field procedure. The "all-bonds" contraint often results in different problems. You will have to play with the relevant parameters, like lincs_order and allowable deviation. On Tue, Jul 21, 2015 at 2:28 PM, Mohsen Ramezanpour <[email protected]> wrote: > Dear Gromacs users, > > I am interested in simulation of lipid bilayers with Gromos96 53a6. > As I understood this force field has been parametrized with reaction field > instead of pme. > > Based on literatures, I have the following .mdp parameters: > But I am not sure of those as my system has lots of LINCS warnings with > these parameters. > > integrator = md > tinit = 0 > dt = 0.002 > nsteps = 50000 > nstcomm = 1 > comm-grps = > > > nstxout = 0 > nstvout = 0 > nstfout = 0 > nstenergy = 100 > nstxtcout = 5000 > xtc-precision = 1000 > energygrps = system > > nstlist = 5 > ns_type = grid > pbc = xyz > rlist = 0.8 > > coulombtype = reaction_field > rcoulomb-switch = 0 > rcoulomb = 1.4 > epsilon_rf = 62 > vdw-type = Cut-off > rvdw-switch = 0 > rvdw = 1.4 > DispCorr = no > > > tcoupl = v-rescale > tc_grps = lipid water_ion > tau_t = 0.1 0.1 > ref_t = 353 353 > Pcoupl = berendsen > pcoupltype = semiisotropic > tau_p = 1.0 1.0 > compressibility = 4.6e-5 4.6e-5 > ref_p = 1.0 1.0 > > > gen_vel = yes > gen_temp = 353 > gen_seed = 17352 > > constraints = all-bonds > constraint-algorithm = Lincs > unconstrained-start = no > shake-tol = 1e-04 > morse = no > > > Interestingly, when I use common Gromos parameters including pme, as > follows, I do not have any LINCS problem with my system. > > integrator = md > tinit = 0 > dt = 0.002 > nsteps = 50000 > pbc = xyz > comm-mode = linear > nstcomm = 1 > comm-grps = system > > > nstxout = 0 > nstvout = 0 > nstfout = 0 > nstlist = 10 > ns_type = grid > nstenergy = 100 > nstxtcout = 5000 > energygrps = system > > > coulombtype = pme > rcoulomb = 1.0 > rlist = 1.0 > vdw-type = cutoff > rvdw = 1.0 > DispCorr = no > table-extension = 1 > > > tcoupl = v-rescale > tc-grps = lipid water_ion > tau-t = 0.1 0.1 > ref-t = 353 353 > Pcoupl = berendsen > Pcoupltype = semiisotropic > ref-p = 1.0 1.0 > tau-p = 1.0 1.0 > compressibility = 4.5e-5 4.5e-5 > > > constraints = all-bonds > constraint-algorithm = Lincs > > > gen_vel = yes > gen_temp = 353 > gen_seed = -1 > > > Since the initial structures are the same, I think my parameters for > reaction field one has problem. I have also tried shorter time steps (even > 0.5 fs) and also started from different initial structures but the problem > still exist. > > I searched the mailing list but I could not find my answer completely. > Please let me know if you have any idea about parameters or if you have any > .mdp file for reaction field (Gromos 53a6). > > Cheers > Mohsen > -- > *Rewards work better than punishment ...* > -- > 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].
