Justin Lemkul <jalemkul@...> writes: > > > On 9/1/15 9:40 AM, Nima Soltani wrote: > > Hi everyone > > I am simulating the interactions between a small peptide and different > > metallic surfaces solvated in TIP3P water. > > So far i have simulated 3 different surfaces correctly , however the last > > surface becames unstable after nearly 2 ns of simulation. > > I did an EM step again and reduced time step to half (i.e. 0.5 fs) however > > it didn't work ... I've even set lincs-warnangle to its maximum value(= > > 90), howeer it failed again . I don't have any idea how to fix it > > > > The surface is Polarizable by using *Drude* oscillators and i think these > > oscillatoras are the cause of problems . > > > > > > Step Time Lambda > > 2270000 2270.00000 0.00000 > > > > Energies (kJ/mol) > > U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 > > 3.87510e+02 6.15054e+01 1.98057e+01 -5.57740e+01 6.96654e+01 > > Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. > > 2.93372e+03 8.97847e+04 -6.19085e+03 -7.47168e+05 2.44969e+03 > > COM Pull En. Potential Kinetic En. Total Energy Temperature > > 1.39457e-03 -6.57708e+05 1.23026e+05 -5.34682e+05 3.09198e+02 > > Pres. DC (bar) Pressure (bar) Constr. rmsd > > -2.03445e+02 -9.16454e+01 1.80260e-06 > > > > > > ------------------------------------------------------- > > Program gmx, VERSION 5.0.5 > > Source code file: > > /share/apps/gromacs-5.0.5/gromacs-5.0.5/src/gromacs/mdlib/constr.c, line: > > 224 > > > > Fatal error: > > Too many LINCS warnings (1000) > > If you know what you are doing you can adjust the lincs warning threshold > > in your mdp file > > or set the environment variable GMX_MAXCONSTRWARN to -1, > > but normally it is better to fix the problem > > For more information and tips for troubleshooting, please check the GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > ------------------------------------------------------- > > Thanks in advance for any suggestions / assistance > > > > You'll have to describe in exact detail what you're doing. It's very easy to > break a polarizable model. What are the sources of the parameters? Have these > parameters been validated in the context of TIP3P? This sounds like a very > weird combination to me, to have part of the system polarizable and the rest not. > > -Justin > I am simulating a peptide near these interfaces and every step of preparing my input files was carefully tested (either by me or by computer :-) ) i am applying a 310K temperature to Drude oscillating particles of the silver ( and Au), while the rest of metal atom types have been frozen. every time the simulation breaks , one oscillator in the metal is moving so fast that it changes it;s angle more than 90 degree !
details of simulation is in the mdp file ; Run parameters integrator = md ; leap-frog integrator nsteps = 10000000 ; 10 ns dt = 0.001 ; 1 fs ;Freeze groups freezegrps = GolPFreeze freezedim = Y Y Y ; Output control nstxout-compressed = 0 nstxout = 10000 ; save coordinates every 10 ps nstvout = 10000 ; save velocities every 10 ps nstenergy = 10000 ; save energies every 10 ps nstlog = 10000 ; update log file every 10 ps ; Bond parameters constraint_algorithm = lincs ; constraints = all-bonds ; ; Neighborsearching cutoff_scheme = Verlet ns_type = grid ; nstlist = 30 ; rcoulomb = 1.2 ; rvdw = 1.2 ; ; Electrostatics coulombtype = PME ; pme_order = 4 fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; Nose-Hoover thermostat tc-grps = Protein Water_and_ions GoldnotFrz GolPFreeze ; tau_t = 0.5 0.5 0.5 0.5 ; ref_t = 310 310 310 0 ; ; Pressure coupling is on pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 1.0 ref_p = 1.0 1.0 compressibility = 0 4.5e-5 refcoord_scaling = com ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; Velocity generation is off ; Pull code pull = umbrella pull_geometry = distance ; simple distance increase pull_dim = N N Y pull_start = yes ; define initial COM distance > 0 pull_ncoords = 1 pull_ngroups = 2 pull_coord1_groups = 1 2 pull_group1_name = Ref pull_group2_name = Protein pull_coord1_rate = 0 pull_coord1_k = 1000 ; kJ mol^-1 nm^-2 pull-coord1-init =0 pull_nstxout = 500 ; every 0.5 ps pull_nstfout = 500 ; every 0.5 ps -- 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.
