[gmx-users] Drug Enzyme Tutorial - mdrun segmentation fault
Tom Joseph
tom-lists at jambon.ll.cx
Wed Apr 19 17:57:12 CEST 2006
This is probably the result of a bug in 3.3, fixed in 3.3.1. Setting
pme_order = 4 is a workaround in case you don't want to upgrade to
3.3.1.
--Tom
On Apr 19, 2006, at 11:05 AM, Zorzan Simone wrote:
> 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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