[gmx-users] energy minimization error
James Lord
jjamesgreen110 at gmail.com
Sun May 17 05:35:23 CEST 2015
Hi Justin
Thanks for this. Can you tell me which step(s) this bond length is
defined???? What should I do (redo) to resolve this issue?
Cheers
James
On Sun, May 17, 2015 at 9:02 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 5/16/15 6:27 AM, James Lord wrote:
>
>> Dear gmx users,
>> I am getting this error, Can anyone help me to get around this?
>> Cheers
>> James
>>
>>
>> Program mdrun, VERSION 4.6.3
>> Source code file: /home/james/gromacs-4.6.3/src/mdlib/domdec.c, line: 6792
>>
>> Fatal error:
>> There is no domain decomposition for 8 nodes that is compatible with the
>> given box and a minimum cell size of 6.93203 nm
>> Change the number of nodes or mdrun option -rdd
>> Look in the log file for details on the domain decomposition
>>
>>
>>
>> Log file opened on Sat May 16 22:15:44 2015
>> Host: james-E530 pid: 22300 nodeid: 0 nnodes: 1
>> Gromacs version: VERSION 4.6.3
>> Precision: single
>> Memory model: 64 bit
>> MPI library: thread_mpi
>> OpenMP support: enabled
>> GPU support: disabled
>> invsqrt routine: gmx_software_invsqrt(x)
>> CPU acceleration: AVX_256
>> FFT library: fftw-3.3.2-sse2
>> Large file support: enabled
>> RDTSCP usage: enabled
>> Built on: Wed Oct 30 18:28:46 NZDT 2013
>> Built by: james at james-E530 [CMAKE]
>> Build OS/arch: Linux 3.11.0-12-generic x86_64
>> Build CPU vendor: GenuineIntel
>> Build CPU brand: Intel(R) Core(TM) i7-3632QM CPU @ 2.20GHz
>> Build CPU family: 6 Model: 58 Stepping: 9
>> Build CPU features: apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr
>> nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1
>> sse4.2 ssse3 tdt x2apic
>> C compiler: /usr/bin/cc GNU cc (Ubuntu/Linaro 4.8.1-10ubuntu8)
>> 4.8.1
>> C compiler flags: -mavx -Wextra -Wno-missing-field-initializers
>> -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unused-parameter
>> -Wno-array-bounds -Wno-maybe-uninitialized -Wno-strict-overflow
>> -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3
>> -DNDEBUG
>>
>>
>> :-) G R O M A C S (-:
>>
>> Gromacs Runs On Most of All Computer Systems
>>
>> :-) VERSION 4.6.3 (-:
>>
>> Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
>> Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
>> Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph
>> Junghans,
>> Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
>> Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
>> Michael Shirts, Alfons Sijbers, Peter Tieleman,
>>
>> Berk Hess, David van der Spoel, and Erik Lindahl.
>>
>> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>> Copyright (c) 2001-2012,2013, The GROMACS development team at
>> Uppsala University & The Royal Institute of Technology, Sweden.
>> 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 Lesser General Public License
>> as published by the Free Software Foundation; either version 2.1
>> of the License, or (at your option) any later version.
>>
>> :-) mdrun (-:
>>
>>
>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>> B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
>> GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
>> molecular simulation
>> J. Chem. Theory Comput. 4 (2008) pp. 435-447
>> -------- -------- --- Thank You --- -------- --------
>>
>>
>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>> D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J.
>> C.
>> Berendsen
>> GROMACS: Fast, Flexible and Free
>> J. Comp. Chem. 26 (2005) pp. 1701-1719
>> -------- -------- --- Thank You --- -------- --------
>>
>>
>> ++++ 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 = steep
>> nsteps = 50000
>> init-step = 0
>> cutoff-scheme = Group
>> ns_type = Grid
>> nstlist = 5
>> ndelta = 2
>> nstcomm = 100
>> comm-mode = Linear
>> nstlog = 1000
>> nstxout = 0
>> nstvout = 0
>> nstfout = 0
>> nstcalcenergy = 100
>> nstenergy = 1000
>> nstxtcout = 0
>> init-t = 0
>> delta-t = 0.001
>> xtcprec = 1000
>> fourierspacing = 0.12
>> nkx = 56
>> nky = 56
>> nkz = 144
>> pme-order = 4
>> ewald-rtol = 1e-05
>> ewald-geometry = 0
>> epsilon-surface = 0
>> optimize-fft = FALSE
>> ePBC = xyz
>> bPeriodicMols = FALSE
>> bContinuation = FALSE
>> bShakeSOR = FALSE
>> etc = No
>> bPrintNHChains = FALSE
>> nsttcouple = -1
>> epc = No
>> epctype = Isotropic
>> nstpcouple = -1
>> tau-p = 1
>> ref-p (3x3):
>> ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>> ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>> ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>> compress (3x3):
>> compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>> compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>> compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>> refcoord-scaling = No
>> posres-com (3):
>> posres-com[0]= 0.00000e+00
>> posres-com[1]= 0.00000e+00
>> posres-com[2]= 0.00000e+00
>> posres-comB (3):
>> posres-comB[0]= 0.00000e+00
>> posres-comB[1]= 0.00000e+00
>> posres-comB[2]= 0.00000e+00
>> verlet-buffer-drift = 0.005
>> rlist = 0.9
>> rlistlong = 1.4
>> nstcalclr = 5
>> rtpi = 0.05
>> coulombtype = PME
>> coulomb-modifier = None
>> rcoulomb-switch = 0
>> rcoulomb = 0.9
>> vdwtype = Cut-off
>> vdw-modifier = None
>> rvdw-switch = 0
>> rvdw = 1.4
>> epsilon-r = 1
>> epsilon-rf = inf
>> tabext = 1
>> implicit-solvent = No
>> gb-algorithm = Still
>> gb-epsilon-solvent = 80
>> nstgbradii = 1
>> rgbradii = 1
>> gb-saltconc = 0
>> gb-obc-alpha = 1
>> gb-obc-beta = 0.8
>> gb-obc-gamma = 4.85
>> gb-dielectric-offset = 0.009
>> sa-algorithm = Ace-approximation
>> sa-surface-tension = 2.05016
>> DispCorr = No
>> bSimTemp = FALSE
>> free-energy = no
>> nwall = 0
>> wall-type = 9-3
>> wall-atomtype[0] = -1
>> wall-atomtype[1] = -1
>> wall-density[0] = 0
>> wall-density[1] = 0
>> wall-ewald-zfac = 3
>> pull = no
>> rotation = FALSE
>> disre = No
>> disre-weighting = Conservative
>> disre-mixed = FALSE
>> dr-fc = 1000
>> dr-tau = 0
>> nstdisreout = 100
>> orires-fc = 0
>> orires-tau = 0
>> nstorireout = 100
>> dihre-fc = 0
>> em-stepsize = 0.01
>> em-tol = 1000
>> 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-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}
>> adress = FALSE
>> userint1 = 0
>> userint2 = 0
>> userint3 = 0
>> userint4 = 0
>> userreal1 = 0
>> userreal2 = 0
>> userreal3 = 0
>> userreal4 = 0
>> grpopts:
>> nrdf: 95838
>> ref-t: 0
>> tau-t: 0
>> anneal: No
>> ann-npoints: 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
>>
>> Initializing Domain Decomposition on 8 nodes
>> Dynamic load balancing: no
>> Will sort the charge groups at every domain (re)decomposition
>> Initial maximum inter charge-group distances:
>> two-body bonded interactions: 6.302 nm, Bond, atoms 8476 8477
>> multi-body bonded interactions: 6.302 nm, Angle, atoms 8476 8477
>>
>
> Bonds shouldn't be 6.3 nm long. Something is wrong with your input
> coordinates.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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