Hi guys, As Justin pointed out, it was the problem with md simulation blowing up. I also had coloumbtype=PME and had to switch to cut-off to make my simulation run faster.
Thanks for all the help. On Thu, Oct 8, 2009 at 11:44 AM, Jochen Hub <joc...@xray.bmc.uu.se> wrote: > > > > delta_t = 0.01 > > You are using a 10 fs timestep!!! That is way too long. Standard is 2 (with > bond constraints). > > > > Yongchul Chung wrote: > >> Hi all, >> >> I am trying to simulate 100 molecules of n-alkane molecules but keep >> receiving LINC errors. >> When I completed steepest descent I received following msg: >> >> Steepest Descents converged to Fmax < 500 in 819 steps >> Potential Energy = 1.7174361e+05 >> Maximum force = 4.4903098e+02 on atom 172 >> Norm of force = 3.0003010e+01 >> >> Then I performed mdrun with the output of this file and gets LINCS >> warning: >> >> >> Input Parameters: >> integrator = md >> nsteps = 8000 >> init_step = 0 >> ns_type = Grid >> nstlist = 10 >> ndelta = 2 >> nstcomm = 1 >> comm_mode = Linear >> nstlog = 10 >> nstxout = 250 >> nstvout = 1000 >> nstfout = 0 >> nstenergy = 10 >> nstxtcout = 0 >> init_t = 0 >> delta_t = 0.01 >> xtcprec = 1000 >> nkx = 125 >> nky = 125 >> nkz = 125 >> pme_order = 4 >> ewald_rtol = 1e-05 >> ewald_geometry = 0 >> epsilon_surface = 0 >> optimize_fft = TRUE >> ePBC = xyz >> bPeriodicMols = FALSE >> bContinuation = FALSE >> bShakeSOR = FALSE >> etc = V-rescale >> epc = No >> epctype = Isotropic >> tau_p = 1 >> ref_p (3x3): >> ref_p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} >> ref_p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} >> ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} >> compress (3x3): >> compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} >> compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} >> compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} >> refcoord_scaling = No >> posres_com (3): >> posres_com[0]= 0.00000e+00 >> posres_com[1]= 0.00000e+00 >> posres_com[2]= 0.00000e+00 >> posres_comB (3): >> posres_comB[0]= 0.00000e+00 >> posres_comB[1]= 0.00000e+00 >> posres_comB[2]= 0.00000e+00 >> andersen_seed = 815131 >> rlist = 1 >> rtpi = 0.05 >> coulombtype = PME >> rcoulomb_switch = 0 >> rcoulomb = 1 >> vdwtype = Cut-off >> rvdw_switch = 0 >> rvdw = 2 >> epsilon_r = 1 >> epsilon_rf = 1 >> tabext = 1 >> implicit_solvent = No >> gb_algorithm = Still >> gb_epsilon_solvent = 80 >> nstgbradii = 1 >> rgbradii = 2 >> gb_saltconc = 0 >> gb_obc_alpha = 1 >> gb_obc_beta = 0.8 >> gb_obc_gamma = 4.85 >> sa_surface_tension = 2.092 >> DispCorr = No >> free_energy = no >> init_lambda = 0 >> sc_alpha = 0 >> sc_power = 0 >> sc_sigma = 0.3 >> delta_lambda = 0 >> nwall = 0 >> wall_type = 9-3 >> wall_atomtype[0] = -1 >> wall_atomtype[1] = -1 >> wall_density[0] = 0 >> wall_density[1] = 0 >> wall_ewald_zfac = 3 >> pull = no >> disre = No >> disre_weighting = Conservative >> disre_mixed = FALSE >> dr_fc = 1000 >> dr_tau = 0 >> nstdisreout = 100 >> orires_fc = 0 >> orires_tau = 0 >> nstorireout = 100 >> dihre-fc = 1000 >> em_stepsize = 0.01 >> em_tol = 10 >> niter = 20 >> fc_stepsize = 0 >> nstcgsteep = 1000 >> nbfgscorr = 10 >> ConstAlg = Lincs >> shake_tol = 0.0001 >> lincs_order = 4 >> lincs_warnangle = 30 >> lincs_iter = 1 >> bd_fric = 0 >> ld_seed = 1993 >> cos_accel = 0 >> deform (3x3): >> deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} >> deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} >> deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} >> userint1 = 0 >> userint2 = 0 >> userint3 = 0 >> userint4 = 0 >> userreal1 = 0 >> userreal2 = 0 >> userreal3 = 0 >> userreal4 = 0 >> grpopts: >> nrdf: 11297 >> ref_t: 300 >> tau_t: 0.1 >> anneal: No >> ann_npoints: 0 >> acc: 0 0 0 >> nfreeze: N N N >> energygrp_flags[ 0]: 0 >> efield-x: >> n = 0 >> efield-xt: >> n = 0 >> efield-y: >> n = 0 >> efield-yt: >> n = 0 >> efield-z: >> n = 0 >> efield-zt: >> n = 0 >> bQMMM = FALSE >> QMconstraints = 0 >> QMMMscheme = 0 >> scalefactor = 1 >> qm_opts: >> ngQM = 0 >> Table routines are used for coulomb: TRUE >> Table routines are used for vdw: FALSE >> Will do PME sum in reciprocal space. >> >> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ >> U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. >> Pedersen >> A smooth particle mesh Ewald method >> J. Chem. Phys. 103 (1995) pp. 8577-8592 >> -------- -------- --- Thank You --- -------- -------- >> >> Using a Gaussian width (1/beta) of 0.320163 nm for Ewald >> Cut-off's: NS: 1 Coulomb: 1 LJ: 2 >> System total charge: -0.000 >> Generated table with 1500 data points for Ewald. >> Tabscale = 500 points/nm >> Generated table with 1500 data points for LJ6. >> Tabscale = 500 points/nm >> Generated table with 1500 data points for LJ12. >> Tabscale = 500 points/nm >> Configuring nonbonded kernels... >> Testing AMD 3DNow support... not present. >> Testing ia32 SSE support... present. >> >> >> Removing pbc first time >> >> Initializing LINear Constraint Solver >> >> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ >> B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije >> LINCS: A Linear Constraint Solver for molecular simulations >> J. Comp. Chem. 18 (1997) pp. 1463-1472 >> -------- -------- --- Thank You --- -------- -------- >> >> The number of constraints is 5500 >> Center of mass motion removal mode is Linear >> We have the following groups for center of mass motion removal: >> 0: rest >> >> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ >> G. Bussi, D. Donadio and M. Parrinello >> Canonical sampling through velocity rescaling >> J. Chem. Phys. 126 (2007) pp. 014101 >> -------- -------- --- Thank You --- -------- -------- >> >> There are: 5600 Atoms >> Max number of connections per atom is 4 >> Total number of connections is 11000 >> Max number of graph edges per atom is 4 >> Total number of graph edges is 11000 >> >> Constraining the starting coordinates (step 0) >> >> Constraining the coordinates at t0-dt (step 0) >> RMS relative constraint deviation after constraining: 6.33e-04 >> Initial temperature: 306.393 K >> >> Started mdrun on node 0 Thu Oct 8 09:58:49 2009 >> >> Step Time Lambda >> 0 0.00000 0.00000 >> >> Grid: 25 x 25 x 25 cells >> >> ------------------------------------------------------- >> Program mdrun, VERSION 4.0.2 >> Source code file: constr.c, line: 136 >> >> Fatal error: >> Too many LINCS warnings (3821) >> 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 >> ------------------------------------------------------- >> >> Can anyone help me to navigate this issue? >> Thanks >> -- >> Yongchul "Greg" Chung >> Graduate Student >> Dept. of Chemical Engineering, Case Western Reserve University >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > -- > --------------------------------------------------- > Dr. Jochen Hub > Molecular Biophysics group > Dept. of Cell & Molecular Biology > Uppsala University. Box 596, 75124 Uppsala, Sweden. > Phone: +46-18-4714451 Fax: +46-18-511755 > > --------------------------------------------------- > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Yongchul "Greg" Chung Graduate Student Dept. of Chemical Engineering, Case Western Reserve University
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