[gmx-users] LINCS error
Yongchul Chung
yxc169 at case.edu
Thu Oct 8 20:11:46 CEST 2009
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 <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
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> gmx-users mailing list gmx-users at 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-request at 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 at 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-request at 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091008/12be8ae5/attachment.html>
More information about the gromacs.org_gmx-users
mailing list