[gmx-users] Drug Enzyme Tutorial - mdrun segmentation fault
Zorzan Simone
zorzan at sci.univr.it
Thu Apr 20 14:08:48 CEST 2006
Hi Tom, and thankyou very much!
The workaround didn't work but I udgraded to Gromacs 3.3.1 and now I get
mdrun running correctly.
-Simone
> 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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