[gmx-users] energy minimization error
Justin Lemkul
jalemkul at vt.edu
Sat May 16 23:03:22 CEST 2015
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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