[gmx-users] LINCS error
Justin A. Lemkul
jalemkul at vt.edu
Thu Oct 8 21:05:50 CEST 2009
Yongchul Chung wrote:
> 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.
>
And it will be substantially less accurate than using PME. I would say Jochen's
advice is the best - reduce the time step to something reasonable, and use PME.
-Justin
> Thanks for all the help.
>
> On Thu, Oct 8, 2009 at 11:44 AM, Jochen Hub <jochen at xray.bmc.uu.se
> <mailto:jochen at 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
> ------------------------------------------------------------------------
>
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>
>
> --
> ---------------------------------------------------
> 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
>
> ---------------------------------------------------
>
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>
>
>
>
> --
> Yongchul "Greg" Chung
> Graduate Student
> Dept. of Chemical Engineering, Case Western Reserve University
>
>
> ------------------------------------------------------------------------
>
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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