[gmx-users] Re: LINCS warnings and box errors
Tsjerk Wassenaar
tsjerkw at gmail.com
Thu Jul 28 10:12:50 CEST 2005
Hi Abel,
Your box seems to be exploding, given the dimensions of the box he's
trying to correct. Your system appears to be unstable, which is the
cause of the error messages, and hence the large log file. Check your
starting configuration for overlaps, water molecules trapped in
isolation and try to energy minimize the system (further). Also check
the potential energy after energy minimization, as it gives a good
clue on the correctness of the setup.
Hope it helps,
Tsjerk
On 7/27/05, abelius <abelius at gmail.com> wrote:
> Dear All,
>
> First off all, I 'am new to gromacs so sorry if I'm asking silly questions.
> Anyway, I'm trying to run a protein in water simulation with some
> counter ions (setup @ bottom of page).
>
> After some time I get:
>
> /Step 46803, time 93.606 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.002085 (between atoms 2880 and 2882) rms 0.000053
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 2880 2882 39.7 0.1001 0.0998 0.1000 /
>
>
> which is ok because the residue in question rotates a lot, but then it
> turns into an error:
>
> /Step 46870, time 93.74 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.924424 (between atoms 2880 and 2881) rms 0.022156
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 2880 2881 90.0 0.1241 0.1924 0.1000
> 2880 2882 90.0 0.1127 0.1895 0.1000
> Constraint error in algorithm Lincs at step 46870
> /
>
> And even later things get much worse:
>
> /Step 46962 Warning: pressure scaling more than 1%, mu: 1.0175 1.0175
> 1.0175
>
> Step 46962, time 93.924 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> max 162420.828125 (between atoms 2873 and 2874) rms 4130.817871
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 503 505 31.2 0.1330 0.1609 0.1330
> 505 506 34.7 0.1000 0.1255 0.1000
> 505 507 62.5 0.1470 0.2549 0.1470
> 507 508 62.8 0.1530 0.2690 0.1530
> 507 520 77.5 0.1530 0.5076 0.1530
> 520 521 69.7 0.1230 0.3968 0.1230
> 520 522 88.5 0.1330 1.4728 0.1330
> ... /
>
>
> Last but not least gromacs starts writing more than 10Gb!! of error
> messages like this:
>
> /t = 93.928 ps: Water molecule starting at atom 28436 can not be settled.
> Check for bad contacts and/or reduce the timestep.Wrote pdb files with
> previous and current coordinates
> Correcting invalid box:
> old box (3x3):
> old box[ 0]={-2.70746e+12, 0.00000e+00, -0.00000e+00}
> old box[ 1]={ 0.00000e+00, -2.71760e+12, -0.00000e+00}
> old box[ 2]={ 0.00000e+00, 0.00000e+00, -2.42469e+12}
>
>
> /
>
> Can someone tell me what I did wrong ?
> And how to stop gromacs from writing more these enormous logfiles?
>
>
> thxn in advance,
> Abel Jonckheer
>
>
>
> My setup:
>
> There are 0 atoms for free energy perturbation
> Input Parameters:
> integrator = md
> nsteps = 500000
> init_step = 0
> ns_type = Grid
> nstlist = 5
> ndelta = 2
> bDomDecomp = FALSE
> decomp_dir = 0
> nstcomm = 1
> nstcheckpoint = 1000
> nstlog = 100
> nstxout = 500
> nstvout = 0
> nstfout = 0
> nstenergy = 100
> nstxtcout = 0
> init_t = 0
> delta_t = 0.002
> xtcprec = 1000
> nkx = 0
> nky = 0
> nkz = 0
> pme_order = 4
> ewald_rtol = 1e-05
> ewald_geometry = 0
> epsilon_surface = 0
> optimize_fft = TRUE
> ePBC = xyz
> bUncStart = FALSE
> bShakeSOR = FALSE
> etc = Berendsen
> epc = Berendsen
> epctype = Isotropic
> tau_p = 0.5
> ref_p (3x3):
> ref_p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00}
> ref_p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00}
> ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}
> compress (3x3):
> compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00}
> compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00}
> compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05}
> andersen_seed = 815131
> rlist = 0.9
> coulombtype = Cut-off
> rcoulomb_switch = 0
> rcoulomb = 0.9
> vdwtype = Cut-off
> rvdw_switch = 0
> rvdw = 1.4
> epsilon_r = 1
> tabext = 1
> gb_algorithm = Still
> nstgbradii = 1
> rgbradii = 2
> gb_saltconc = 0
> implicit_solvent = No
> DispCorr = No
> fudgeQQ = 1
> free_energy = no
> init_lambda = 0
> sc_alpha = 0
> sc_sigma = 0.3
> delta_lambda = 0
> 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
> dihre-tau = 0
> nstdihreout = 100
> 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_temp = 300
> bd_fric = 0
> ld_seed = 1993
> cos_accel = 0
> userint1 = 0
> userint2 = 0
> userint3 = 0
> userint4 = 0
> userreal1 = 0
> userreal2 = 0
> userreal3 = 0
> userreal4 = 0
> grpopts:
> nrdf: 6593.65 50241.3 17.9991
> ref_t: 300 300 300
> tau_t: 0.1 0.1 0.1
> anneal: No No No
> ann_npoints: 0 0 0
> acc: 0 0 0
> nfreeze: N N N
> energygrp_excl[ 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
> CPU= 0, lastcg= 9856, targetcg= 4928, myshift= 0
> nsb->shift = 1, nsb->bshift= 0
> Neighbor Search Blocks
> nsb->nodeid: 0
> nsb->nnodes: 1
> nsb->cgtotal: 9857
> nsb->natoms: 28450
> nsb->shift: 1
> nsb->bshift: 0
> Nodeid index homenr cgload workload
> 0 0 28450 9857 9857
>
> Max number of graph edges per atom is 10
> Table routines are used for coulomb: FALSE
> Table routines are used for vdw: FALSE
> Cut-off's: NS: 0.9 Coulomb: 0.9 LJ: 1.4
> Generated table with 500 data points for COUL.
> Tabscale = 500 points/nm
> Generated table with 500 data points for LJ6.
> Tabscale = 500 points/nm
> Generated table with 500 data points for LJ12.
> Tabscale = 500 points/nm
> Going to determine what solvent types we have.
> There are 8381 molecules, 9857 charge groups and 28450 atoms
> There are 0 optimized solvent molecules on node 0
> There are 8374 optimized water molecules on node 0
> Center of mass motion removal mode is Linear
> We have the following groups for center of mass motion removal:
> 0: rest, initial mass: 188046
> There are: 28450 Atom
> Removing pbc first time
> Done rmpbc
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