[gmx-users] LINCS warnings and box errors
abelius
abelius at gmail.com
Wed Jul 27 11:30:57 CEST 2005
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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