Hi all,<br><br>I am trying to simulate 100 molecules of n-alkane molecules but keep receiving LINC errors.<br>When I completed steepest descent I received following msg:<br><br><div style="margin-left: 40px;">Steepest Descents converged to Fmax < 500 in 819 steps<br>
</div><div style="margin-left: 40px;">Potential Energy = 1.7174361e+05<br></div><div style="margin-left: 40px;">Maximum force = 4.4903098e+02 on atom 172<br></div><div style="margin-left: 40px;">Norm of force = 3.0003010e+01<br clear="all">
</div><br>Then I performed mdrun with the output of this file and gets LINCS warning:<br><br><br><div style="margin-left: 40px;">Input Parameters:<br> integrator = md<br> nsteps = 8000<br> init_step = 0<br>
ns_type = Grid<br> nstlist = 10<br> ndelta = 2<br> nstcomm = 1<br> comm_mode = Linear<br> nstlog = 10<br> nstxout = 250<br>
nstvout = 1000<br> nstfout = 0<br> nstenergy = 10<br> nstxtcout = 0<br> init_t = 0<br> delta_t = 0.01<br> xtcprec = 1000<br>
nkx = 125<br> nky = 125<br> nkz = 125<br> pme_order = 4<br> ewald_rtol = 1e-05<br> ewald_geometry = 0<br> epsilon_surface = 0<br>
optimize_fft = TRUE<br> ePBC = xyz<br> bPeriodicMols = FALSE<br> bContinuation = FALSE<br> bShakeSOR = FALSE<br> etc = V-rescale<br> epc = No<br>
epctype = Isotropic<br> tau_p = 1<br> ref_p (3x3):<br> ref_p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br> ref_p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br> ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br>
compress (3x3):<br> compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br> compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br> compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br>
refcoord_scaling = No<br> posres_com (3):<br> posres_com[0]= 0.00000e+00<br> posres_com[1]= 0.00000e+00<br> posres_com[2]= 0.00000e+00<br> posres_comB (3):<br> posres_comB[0]= 0.00000e+00<br>
posres_comB[1]= 0.00000e+00<br> posres_comB[2]= 0.00000e+00<br> andersen_seed = 815131<br> rlist = 1<br> rtpi = 0.05<br> coulombtype = PME<br> rcoulomb_switch = 0<br>
rcoulomb = 1<br> vdwtype = Cut-off<br> rvdw_switch = 0<br> rvdw = 2<br> epsilon_r = 1<br> epsilon_rf = 1<br> tabext = 1<br>
implicit_solvent = No<br> gb_algorithm = Still<br> gb_epsilon_solvent = 80<br> nstgbradii = 1<br> rgbradii = 2<br> gb_saltconc = 0<br> gb_obc_alpha = 1<br>
gb_obc_beta = 0.8<br> gb_obc_gamma = 4.85<br> sa_surface_tension = 2.092<br> DispCorr = No<br> free_energy = no<br> init_lambda = 0<br> sc_alpha = 0<br>
sc_power = 0<br> sc_sigma = 0.3<br> delta_lambda = 0<br> nwall = 0<br> wall_type = 9-3<br> wall_atomtype[0] = -1<br> wall_atomtype[1] = -1<br>
wall_density[0] = 0<br> wall_density[1] = 0<br> wall_ewald_zfac = 3<br> pull = no<br> disre = No<br> disre_weighting = Conservative<br> disre_mixed = FALSE<br>
dr_fc = 1000<br> dr_tau = 0<br> nstdisreout = 100<br> orires_fc = 0<br> orires_tau = 0<br> nstorireout = 100<br> dihre-fc = 1000<br>
em_stepsize = 0.01<br> em_tol = 10<br> niter = 20<br> fc_stepsize = 0<br> nstcgsteep = 1000<br> nbfgscorr = 10<br> ConstAlg = Lincs<br>
shake_tol = 0.0001<br> lincs_order = 4<br> lincs_warnangle = 30<br> lincs_iter = 1<br> bd_fric = 0<br> ld_seed = 1993<br> cos_accel = 0<br>
deform (3x3):<br> deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br> deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br> deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br> userint1 = 0<br>
userint2 = 0<br> userint3 = 0<br> userint4 = 0<br> userreal1 = 0<br> userreal2 = 0<br> userreal3 = 0<br> userreal4 = 0<br>grpopts:<br>
nrdf: 11297<br> ref_t: 300<br> tau_t: 0.1<br>anneal: No<br>ann_npoints: 0<br> acc: 0 0 0<br> nfreeze: N N N<br>
energygrp_flags[ 0]: 0<br> efield-x:<br> n = 0<br> efield-xt:<br> n = 0<br> efield-y:<br> n = 0<br> efield-yt:<br> n = 0<br> efield-z:<br> n = 0<br> efield-zt:<br> n = 0<br> bQMMM = FALSE<br>
QMconstraints = 0<br> QMMMscheme = 0<br> scalefactor = 1<br>qm_opts:<br> ngQM = 0<br>Table routines are used for coulomb: TRUE<br>Table routines are used for vdw: FALSE<br>
Will do PME sum in reciprocal space.<br><br>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br>U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen <br>A smooth particle mesh Ewald method<br>
J. Chem. Phys. 103 (1995) pp. 8577-8592<br>-------- -------- --- Thank You --- -------- --------<br><br>Using a Gaussian width (1/beta) of 0.320163 nm for Ewald<br>Cut-off's: NS: 1 Coulomb: 1 LJ: 2<br>System total charge: -0.000<br>
Generated table with 1500 data points for Ewald.<br>Tabscale = 500 points/nm<br>Generated table with 1500 data points for LJ6.<br>Tabscale = 500 points/nm<br>Generated table with 1500 data points for LJ12.<br>Tabscale = 500 points/nm<br>
Configuring nonbonded kernels...<br>Testing AMD 3DNow support... not present.<br>Testing ia32 SSE support... present.<br><br><br>Removing pbc first time<br><br>Initializing LINear Constraint Solver<br><br>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br>
B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije<br>LINCS: A Linear Constraint Solver for molecular simulations<br>J. Comp. Chem. 18 (1997) pp. 1463-1472<br>-------- -------- --- Thank You --- -------- --------<br>
<br>The number of constraints is 5500<br>Center of mass motion removal mode is Linear<br>We have the following groups for center of mass motion removal:<br> 0: rest<br><br>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br>
G. Bussi, D. Donadio and M. Parrinello<br>Canonical sampling through velocity rescaling<br>J. Chem. Phys. 126 (2007) pp. 014101<br>-------- -------- --- Thank You --- -------- --------<br><br>There are: 5600 Atoms<br>Max number of connections per atom is 4<br>
Total number of connections is 11000<br>Max number of graph edges per atom is 4<br>Total number of graph edges is 11000<br><br>Constraining the starting coordinates (step 0)<br><br>Constraining the coordinates at t0-dt (step 0)<br>
RMS relative constraint deviation after constraining: 6.33e-04<br>Initial temperature: 306.393 K<br><br>Started mdrun on node 0 Thu Oct 8 09:58:49 2009<br><br> Step Time Lambda<br> 0 0.00000 0.00000<br>
<br>Grid: 25 x 25 x 25 cells<br><br>-------------------------------------------------------<br>Program mdrun, VERSION 4.0.2<br>Source code file: constr.c, line: 136<br><br>Fatal error:<br>Too many LINCS warnings (3821)<br>
If you know what you are doing you can adjust the lincs warning threshold in your mdp file<br>or set the environment variable GMX_MAXCONSTRWARN to -1,<br>but normally it is better to fix the problem<br>-------------------------------------------------------<br>
</div><br>Can anyone help me to navigate this issue?<br>Thanks<br>-- <br>Yongchul "Greg" Chung<br>Graduate Student<br>Dept. of Chemical Engineering, Case Western Reserve University<br>