[gmx-users] Re: LINCS warnings and box errors
abelius
abelius at gmail.com
Thu Aug 25 08:38:28 CEST 2005
Hi Tsjerk,
Its been a while and since then I've tried a whole series of different
setups, I include extra minimalization steps, removed potentially
problematic waters, checked the potential energy, did a run without
p-coupling etc.
I've got as far that in the logfile there are no more warnings about box
errors, but after about 180ps I still get a lot of LINCS warnings until
the md crashes.
I thought center of mass translation could be the problem so I tried
runs with different nstcomm values, but still no effect.
In the end I simple gave up and tried to run the demo shipped with
gromacs again, but this time for 1ns. Looking at the trajectory the
cpeptide bounces around a lot and even leaves the box at around 900ps.
Do you have any idea how this can be ?
Thnx in advance,
Abel Jonckheer
Tsjerk Wassenaar wrote:
>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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