[gmx-users] Drug Enzyme Tutorial - mdrun segmentation fault
Zorzan Simone
zorzan at sci.univr.it
Wed Apr 19 17:05:19 CEST 2006
Hi all, I am trying to do the Drug Enzyme tutorial (trp_drug_tutor.pdf),
on a linux box (suse 10.0) and Gromacs 3.3.
Everything is fine until this command:
nohup mdrun -s trp_pr.tpr -o trp_pr.trr -c trp_b4md.gro -g pr.log -e pr.edr
That ends abnormally with a segmentation fault.
I searched the mailing list archive but I didn't find anything helpful.
Has anybody tried this tutorial with Gromacs 3.3 (it's tested on 3.2.1)?
Any help is greatly appreciated.
Zorzan Simone.
pr.mdp, mdout.mdp and pr.log follows.
============================ pr.mdp ========================
title = trp_drg
warnings = 10
cpp = /lib/cpp ; location of cpp on SGI
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 10000 ; total 20.0 ps.
nstcomm =1
nstxout = 250 ; output coordinates every 0.5 ps
nstvout = 1000 ; output velocities every 2.0 ps
nstfout =0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 0.9
fourierspacing = 0.12
fourier_nx =0
fourier_ny =0
fourier_nz =0
pme_order =6
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in four groups
Tcoupl = berendsen
tau_t = 0.1 0.1 0.1 0.1
tc_grps = protein sol IN4 Cl
ref_t = 300 300 300 300
; Pressure coupling is on
Pcoupl = berendsen
pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
============================== mdout.mdp ======================
;
; File 'mdout.mdp' was generated
; By user: simone (1000)
; On host: linux
; At date: Wed Apr 19 16:52:27 2006
;
; VARIOUS PREPROCESSING OPTIONS
title = trp_drg
; Preprocessor - specify a full path if necessary.
cpp = /lib/cpp
include =
define = -DPOSRES
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit = 0
dt = 0.002
nsteps = 10000
; For exact run continuation or redoing part of a run
init_step = 0
; mode for center of mass motion removal
comm-mode = Linear
; number of steps for center of mass motion removal
nstcomm = 1
; group(s) for center of mass motion removal
comm-grps =
; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric = 0
ld-seed = 1993
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol = 10
emstep = 0.01
; Max number of iterations in relax_shells
niter = 20
; Step size (ps^2) for minimization of flexible constraints
fcstep = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep = 1000
nbfgscorr = 10
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 250
nstvout = 1000
nstfout = 0
; Checkpointing helps you continue after crashes
nstcheckpoint = 1000
; Output frequency for energies to log file and energy file
nstlog = 10
nstenergy = 10
; Output frequency and precision for xtc file
nstxtcout = 0
xtc-precision = 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps =
; Selection of energy groups
energygrps =
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 10
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc = xyz
; nblist cut-off
rlist = 0.9
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 0.9
; Relative dielectric constant for the medium and the reaction field
epsilon_r = 1
epsilon_rf = 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw-switch = 0
rvdw = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = No
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; Seperate tables between energy group pairs
energygrp_table =
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters
pme_order = 6
ewald_rtol = 1e-5
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = yes
; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 2
; Salt concentration in M for Generalized Born models
gb_saltconc = 0
; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
implicit_solvent = No
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl = berendsen
; Groups to couple separately
tc_grps = protein sol IN4 Cl
; Time constant (ps) and reference temperature (K)
tau_t = 0.1 0.1 0.1 0.1
ref_t = 300 300 300 300
; Pressure coupling
Pcoupl = berendsen
pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Random seed for Andersen thermostat
andersen_seed = 815131
; OPTIONS FOR QMMM calculations
QMMM = no
; Groups treated Quantum Mechanically
QMMM-grps =
; QM method
QMmethod =
; QMMM scheme
QMMMscheme = normal
; QM basisset
QMbasis =
; QM charge
QMcharge =
; QM multiplicity
QMmult =
; Surface Hopping
SH =
; CAS space options
CASorbitals =
CASelectrons =
SAon =
SAoff =
SAsteps =
; Scale factor for MM charges
MMChargeScaleFactor = 1
; Optimization of QM subsystem
bOPT =
bTS =
; SIMULATED ANNEALING
; Type of annealing for each temperature group (no/single/periodic)
annealing =
; Number of time points to use for specifying annealing in each group
annealing_npoints =
; List of times at the annealing points for each group
annealing_time =
; Temp. at each annealing point, for each group.
annealing_temp =
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
; OPTIONS FOR BONDS
constraints = all-bonds
; Type of constraint algorithm
constraint-algorithm = Lincs
; Do not constrain the start configuration
unconstrained-start = no
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR = no
; Relative tolerance of shake
shake-tol = 1e-04
; Highest order in the expansion of the constraint coupling matrix
lincs-order = 4
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve energy in NVE runs.
; For energy minimization with constraints it should be 4 to 8.
lincs-iter = 1
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs-warnangle = 30
; Convert harmonic bonds to morse potentials
morse = no
; ENERGY GROUP EXCLUSIONS
; Pairs of energy groups for which all non-bonded interactions are excluded
energygrp_excl =
; NMR refinement stuff
; Distance restraints type: No, Simple or Ensemble
disre = No
; Force weighting of pairs in one distance restraint: Conservative or Equal
disre-weighting = Conservative
; Use sqrt of the time averaged times the instantaneous violation
disre-mixed = no
disre-fc = 1000
disre-tau = 0
; Output frequency for pair distances to energy file
nstdisreout = 100
; Orientation restraints: No or Yes
orire = no
; Orientation restraints force constant and tau for time averaging
orire-fc = 0
orire-tau = 0
orire-fitgrp =
; Output frequency for trace(SD) and S to energy file
nstorireout = 100
; Dihedral angle restraints: No, Simple or Ensemble
dihre = No
dihre-fc = 1000
dihre-tau = 0
; Output frequency for dihedral values to energy file
nstdihreout = 100
; Free energy control stuff
free-energy = no
init-lambda = 0
delta-lambda = 0
sc-alpha = 0
sc-power = 1
sc-sigma = 0.3
; Non-equilibrium MD stuff
acc-grps =
accelerate =
freezegrps =
freezedim =
cos-acceleration = 0
deform =
; Electric fields
; Format is number of terms (int) and for all terms an amplitude (real)
; and a phase angle (real)
E-x =
E-xt =
E-y =
E-yt =
E-z =
E-zt =
; User defined thingies
user1-grps =
user2-grps =
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
============================== pr.log =========================
Log file opened on Wed Apr 19 16:53:02 2006
Host: linux pid: 8362 nodeid: 0 nnodes: 1
The Gromacs distribution was built Tue Oct 11 13:51:00 CEST 2005 by
root at oxygen (Linux 2.6.9-11.ELsmp i686)
:-) G R O M A C S (-:
Gravel Rubs Often Many Awfully Cauterized Sores
:-) VERSION 3.3 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2004, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun (-:
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
-------- -------- --- Thank You --- -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
-------- -------- --- Thank You --- -------- --------
Input Parameters:
integrator = md
nsteps = 10000
init_step = 0
ns_type = Grid
nstlist = 10
ndelta = 2
bDomDecomp = FALSE
decomp_dir = 0
nstcomm = 1
comm_mode = Linear
nstcheckpoint = 1000
nstlog = 10
nstxout = 250
nstvout = 1000
nstfout = 0
nstenergy = 10
nstxtcout = 0
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 50
nky = 48
nkz = 42
pme_order = 6
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 = PME
rcoulomb_switch = 0
rcoulomb = 0.9
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 0.9
epsilon_r = 1
epsilon_rf = 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_power = 1
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 = 1e-04
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: 4166.57 24921.4 66.9931 26.9972
ref_t: 300 300 300 300
tau_t: 0.1 0.1 0.1 0.1
anneal: No No No No
ann_npoints: 0 0 0 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
CPU= 0, lastcg= 5430, targetcg= 2715, myshift= 0
nsb->shift = 1, nsb->bshift= 0
Neighbor Search Blocks
nsb->nodeid: 0
nsb->nnodes: 1
nsb->cgtotal: 5431
nsb->natoms: 14604
nsb->shift: 1
nsb->bshift: 0
Nodeid index homenr cgload workload
0 0 14604 5431 5431
Max number of graph edges per atom is 4
Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
Using a Gaussian width (1/beta) of 0.288146 nm for Ewald
Cut-off's: NS: 0.9 Coulomb: 0.9 LJ: 0.9
System total charge: 0.000
Generated table with 949 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 949 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 949 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 500 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 500 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 500 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Enabling SPC water optimization for 4154 molecules.
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 --- -------- --------
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest, initial mass: 98823
There are: 14604 Atoms
Removing pbc first time
Done rmpbc
Constraining the starting coordinates (step -2)
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak
Molecular dynamics with coupling to an external bath
J. Chem. Phys. 81 (1984) pp. 3684-3690
-------- -------- --- Thank You --- -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------
++++ 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 --- -------- --------
Initializing LINear Constraint Solver
number of constraints is 2165
average number of constraints coupled to one constraint is 2.9
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.045226 153 154 0.006870
After LINCS 0.000787 2103 2107 0.000129
Going to use C-settle (4154 waters)
wo = 0.888096, wh =0.0559521, wohh = 18.0154, rc = 0.08165, ra = 0.00646074
rb = 0.0512738, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1
Constraining the coordinates at t0-dt (step -1)
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.090682 1135 1136 0.016874
After LINCS 0.000242 1878 1880 0.000041
Started mdrun on node 0 Wed Apr 19 16:53:03 2006
Initial temperature: 298.34 K
Step Time Lambda
0 0.00000 0.00000
Grid: 13 x 12 x 10 cells
Configuring nonbonded kernels...
Testing AMD 3DNow support... present.
Testing ia32 SSE support... present.
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.102216 1168 1169 0.011717
After LINCS 0.000204 2103 2107 0.000042
Energies (kJ/mol)
Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
1.30666e+03 9.31797e+02 3.00381e+02 1.67409e+03 2.50861e+04
LJ (SR) Coulomb (SR) Coul. recip. Position Rest. Potential
1.81245e+04 -2.01012e+05 -5.00385e+04 6.36238e-01 -2.03627e+05
Kinetic En. Total Energy Temperature Pressure (bar)
4.10711e+04 -1.62556e+05 3.38543e+02 -3.99460e+03
Step 5, time 0.01 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.001332 (between atoms 1948 and 1949) rms 0.000094
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1743 1745 33.0 0.1000 0.1000 0.1000
Step 6, time 0.012 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.001928 (between atoms 1948 and 1949) rms 0.000121
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
125 126 30.5 0.1000 0.1000 0.1000
1743 1745 37.8 0.1000 0.0999 0.1000
Step 7, time 0.014 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.001687 (between atoms 1948 and 1949) rms 0.000134
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1190 1191 30.9 0.1000 0.1000 0.1000
1743 1745 34.5 0.0999 0.1000 0.1000
Step 9, time 0.018 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.002565 (between atoms 1454 and 1455) rms 0.000171
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1454 1455 30.7 0.1002 0.1003 0.1000
Step Time Lambda
10 0.02000 0.00000
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.376663 1454 1455 0.032984
After LINCS 0.003488 1454 1455 0.000205
Step 10, time 0.02 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.003488 (between atoms 1454 and 1455) rms 0.000205
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
893 894 30.1 0.1000 0.1000 0.1000
1454 1455 37.0 0.1003 0.1003 0.1000
1656 1657 31.1 0.1000 0.1000 0.1000
1838 1839 30.8 0.1001 0.1001 0.1000
2038 2041 30.6 0.1000 0.0999 0.1000
Energies (kJ/mol)
Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
1.32695e+04 1.90899e+03 5.23652e+03 3.16260e+03 2.51121e+04
LJ (SR) Coulomb (SR) Coul. recip. Position Rest. Potential
4.45049e+04 -1.22149e+05 -3.77454e+04 2.75519e+02 -6.64239e+04
Kinetic En. Total Energy Temperature Pressure (bar)
4.87645e+05 4.21221e+05 4.01959e+03 1.49701e+04
Step 11, time 0.022 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.002203 (between atoms 1610 and 1611) rms 0.000207
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1454 1455 38.4 0.1004 0.1000 0.1000
1656 1657 33.4 0.1001 0.1000 0.1000
1838 1839 36.1 0.1001 0.1002 0.1000
Step 12, time 0.024 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.002162 (between atoms 1610 and 1611) rms 0.000208
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1454 1455 30.4 0.1001 0.0998 0.1000
1656 1657 31.4 0.1001 0.1000 0.1000
1838 1839 37.1 0.1003 0.1002 0.1000
Step 13, time 0.026 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 1.836471 (between atoms 1743 and 1745) rms 0.051291
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1743 1744 89.9 0.1002 0.2524 0.1000
1743 1745 90.1 0.1001 0.2836 0.1000
1838 1839 34.6 0.1003 0.0999 0.1000
Constraint error in algorithm Lincs at step 13
Step 14, time 0.028 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.003903 (between atoms 1741 and 1743) rms 0.000237
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1743 1744 43.7 0.2528 0.1001 0.1000
1743 1745 44.1 0.2841 0.1000 0.1000
Step 15, time 0.03 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.982324 (between atoms 1743 and 1745) rms 0.025712
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1743 1744 90.0 0.1003 0.1683 0.1000
1743 1745 90.0 0.1002 0.1982 0.1000
Constraint error in algorithm Lincs at step 15
Step 16, time 0.032 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.038037 (between atoms 1743 and 1745) rms 0.000980
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
125 126 30.6 0.1002 0.0999 0.1000
1190 1191 37.5 0.1002 0.0999 0.1000
1743 1744 70.5 0.1686 0.0979 0.1000
1743 1745 52.7 0.1986 0.0962 0.1000
1808 1809 32.7 0.1002 0.1000 0.1000
Step 17, time 0.034 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.871170 (between atoms 1743 and 1745) rms 0.026058
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1190 1191 37.4 0.1001 0.0998 0.1000
1454 1455 36.9 0.1004 0.1004 0.1000
1743 1744 89.9 0.0981 0.1843 0.1000
1743 1745 90.0 0.0964 0.1871 0.1000
1808 1809 36.6 0.1002 0.1000 0.1000
Constraint error in algorithm Lincs at step 17
Step 18, time 0.036 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.017829 (between atoms 1743 and 1744) rms 0.000566
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1454 1455 39.8 0.1007 0.1004 0.1000
1743 1744 48.2 0.1848 0.0982 0.1000
1743 1745 66.1 0.1876 0.0989 0.1000
1808 1809 34.7 0.1003 0.1001 0.1000
Step 19, time 0.038 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.397266 (between atoms 1743 and 1745) rms 0.008560
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1454 1455 38.3 0.1007 0.0998 0.1000
1743 1744 63.4 0.0985 0.0978 0.1000
1743 1745 90.0 0.0992 0.1397 0.1000
1808 1809 35.4 0.1003 0.0999 0.1000
1838 1839 34.6 0.1005 0.1005 0.1000
Step Time Lambda
20 0.04000 0.00000
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 1.795489 1743 1745 0.057160
After LINCS 0.038636 1743 1745 0.001170
Step 20, time 0.04 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.038636 (between atoms 1743 and 1745) rms 0.001170
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1743 1744 69.5 0.0981 0.1032 0.1000
1743 1745 71.6 0.1401 0.1039 0.1000
1808 1809 37.3 0.1002 0.0998 0.1000
1838 1839 43.2 0.1008 0.1008 0.1000
Energies (kJ/mol)
Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
3.43370e+04 3.98299e+03 9.19572e+03 6.03039e+03 2.40893e+04
LJ (SR) Coulomb (SR) Coul. recip. Position Rest. Potential
1.12548e+05 -1.00249e+05 -3.01319e+04 9.44273e+03 6.92452e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.21696e+06 1.28621e+06 1.00313e+04 5.09390e+04
Step 21, time 0.042 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.312929 (between atoms 1743 and 1745) rms 0.006805
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1743 1744 90.0 0.1035 0.0957 0.1000
1743 1745 89.9 0.1042 0.1313 0.1000
1808 1809 30.9 0.1001 0.0999 0.1000
1838 1839 42.7 0.1011 0.0998 0.1000
Step 22, time 0.044 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.194893 (between atoms 1743 and 1745) rms 0.005786
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1656 1657 35.4 0.1004 0.0999 0.1000
1743 1744 89.9 0.0960 0.1184 0.1000
1743 1745 90.1 0.1317 0.1195 0.1000
Large VCM(group rest): 0.00142, -0.00085, 0.00433, ekin-cm:
1.06142e+00
Step 23, time 0.046 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.114104 (between atoms 1743 and 1745) rms 0.002721
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1190 1191 30.7 0.1005 0.1002 0.1000
1656 1657 40.6 0.1002 0.0996 0.1000
1743 1744 36.0 0.1187 0.0967 0.1000
1743 1745 90.2 0.1199 0.1114 0.1000
2038 2039 43.5 0.1003 0.0989 0.1000
t = 0.046 ps: Water molecule starting at atom 5140 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with
previous and current coordinates
Step 24, time 0.048 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.235185 (between atoms 1743 and 1745) rms 0.005153
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1454 1455 35.4 0.1004 0.1004 0.1000
1656 1657 31.6 0.0999 0.0996 0.1000
1743 1744 41.3 0.0970 0.1011 0.1000
1743 1745 89.9 0.1118 0.1235 0.1000
2038 2041 44.4 0.1027 0.1027 0.1000
Step 25, time 0.05 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.015890 (between atoms 2038 and 2041) rms 0.000795
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1190 1191 36.1 0.1004 0.1000 0.1000
1454 1455 39.8 0.1007 0.1004 0.1000
1743 1744 52.8 0.1014 0.1005 0.1000
1743 1745 46.4 0.1239 0.0999 0.1000
1808 1809 39.1 0.1004 0.1002 0.1000
1948 1949 30.1 0.1003 0.0999 0.1000
2038 2041 38.1 0.1030 0.1016 0.1000
t = 0.050 ps: Water molecule starting at atom 5974 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with
previous and current coordinates
Step 26, time 0.052 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.143224 (between atoms 1743 and 1744) rms 0.003191
bonds t
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