[gmx-users] Water molecule starting at atom 39087 can not be settled
Justin Lemkul
jalemkul at vt.edu
Tue Mar 21 23:54:08 CET 2017
On 3/21/17 6:51 PM, liming_52 wrote:
> Dear Gromacs users,I am trying to run a md using 4n6p.cif obtained from PDB with a ligand. I converted the file into pdb format using DS4.1, and got the file named lactoferrin.pdb. When I directly run
> the command "gmx mdrun -v -deffnm em", the program runs and produces the information as follows:
> :-) GROMACS - gmx mdrun, VERSION 5.1.2 (-:
>
> GROMACS is written by:
> Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
> Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
> Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen
> Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner
> Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
> Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
> Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
> Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf
> and the project leaders:
> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
>
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2015, The GROMACS development team at
> Uppsala University, Stockholm University and
> the Royal Institute of Technology, Sweden.
> check out http://www.gromacs.org for more information.
>
> GROMACS 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.
>
> GROMACS: gmx mdrun, VERSION 5.1.2
> Executable: /usr/bin/gmx
> Data prefix: /usr
> Command line:
> gmx mdrun -v -deffnm em
>
>
> Running on 1 node with total 12 cores, 24 logical cores
> Hardware detected:
> CPU info:
> Vendor: GenuineIntel
> Brand: Intel(R) Xeon(R) CPU E5-2620 v2 @ 2.10GHz
> SIMD instructions most likely to fit this hardware: AVX_256
> SIMD instructions selected at GROMACS compile time: SSE2
>
> Compiled SIMD instructions: SSE2, GROMACS could use AVX_256 on this machine, which is better
>
> Reading file em.tpr, VERSION 5.1.2 (single precision)
>
> Will use 18 particle-particle and 6 PME only ranks
> This is a guess, check the performance at the end of the log file
> Using 24 MPI threads
> Using 1 OpenMP thread per tMPI thread
>
>
> Steepest Descents:
> Tolerance (Fmax) = 1.00000e+03
> Number of steps = 50000
> Step= 0, Dmax= 1.0e-03 nm, Epot= 2.62236e+13 Fmax= 1.19534e+16, atom= 3295
> Step= 1, Dmax= 1.0e-03 nm, Epot= 1.08905e+13 Fmax= 4.61331e+15, atom= 3295
> Step= 2, Dmax= 1.2e-03 nm, Epot= 4.10454e+12 Fmax= 1.60266e+15, atom= 3295
> Step= 3, Dmax= 1.4e-03 nm, Epot= 1.40137e+12 Fmax= 5.00036e+14, atom= 3295
> Step= 4, Dmax= 1.7e-03 nm, Epot= 4.33654e+11 Fmax= 1.40069e+14, atom= 3295
> Step= 5, Dmax= 2.1e-03 nm, Epot= 1.22200e+11 Fmax= 3.52752e+13, atom= 3295
> Step= 6, Dmax= 2.5e-03 nm, Epot= 3.18990e+10 Fmax= 8.01234e+12, atom= 3295
> Step= 7, Dmax= 3.0e-03 nm, Epot= 8.21424e+09 Fmax= 1.64883e+12, atom= 3295
> Step= 8, Dmax= 3.6e-03 nm, Epot= 2.50045e+09 Fmax= 3.09257e+11, atom= 3295
> Step= 9, Dmax= 4.3e-03 nm, Epot= 9.40257e+08 Fmax= 6.82365e+10, atom= 3279
> Step= 10, Dmax= 5.2e-03 nm, Epot= 2.72792e+08 Fmax= 1.39988e+10, atom= 3279
> Step= 11, Dmax= 6.2e-03 nm, Epot= 5.92206e+07 Fmax= 2.62182e+09, atom= 3279
> Step= 12, Dmax= 7.4e-03 nm, Epot= 1.69891e+07 Fmax= 4.55609e+08, atom= 3279
> Step= 13, Dmax= 8.9e-03 nm, Epot= 4.88134e+06 Fmax= 1.13133e+08, atom= 3296
> Step= 14, Dmax= 1.1e-02 nm, Epot= 1.86164e+06 Fmax= 3.65858e+07, atom= 3296
> Step= 15, Dmax= 1.3e-02 nm, Epot= 6.44202e+05 Fmax= 1.40616e+07, atom= 3296
> Step= 16, Dmax= 1.5e-02 nm, Epot= 2.16177e+05 Fmax= 4.49293e+06, atom= 3294
> Step= 17, Dmax= 1.8e-02 nm, Epot= 2.88800e+04 Fmax= 2.99167e+06, atom= 134
> Step= 18, Dmax= 2.2e-02 nm, Epot= -3.56134e+04 Fmax= 2.53958e+06, atom= 3296
> Step= 19, Dmax= 2.7e-02 nm, Epot= -7.50786e+04 Fmax= 5.14618e+06, atom= 3296
> Step= 20, Dmax= 3.2e-02 nm, Epot= -1.33736e+05 Fmax= 7.43406e+05, atom= 134
> Step= 21, Dmax= 3.8e-02 nm, Epot= -1.68139e+05 Fmax= 6.44435e+06, atom= 3296
> Step= 22, Dmax= 4.6e-02 nm, Epot= -2.39673e+05 Fmax= 3.99299e+05, atom= 3296
> Step= 23, Dmax= 5.5e-02 nm, Epot= -3.07273e+05 Fmax= 1.60934e+06, atom= 3296
> Step= 24, Dmax= 6.6e-02 nm, Epot= -3.25923e+05 Fmax= 2.64244e+05, atom= 3296
> Step= 26, Dmax= 4.0e-02 nm, Epot= -3.66840e+05 Fmax= 1.58505e+05, atom= 1346
> Step= 27, Dmax= 4.8e-02 nm, Epot= -3.98127e+05 Fmax= 6.82470e+05, atom= 134
> Step= 28, Dmax= 5.7e-02 nm, Epot= -4.11327e+05 Fmax= 1.87577e+05, atom= 3297
> Step= 29, Dmax= 6.9e-02 nm, Epot= -4.41304e+05 Fmax= 3.09908e+05, atom= 3297
> Step= 30, Dmax= 8.2e-02 nm, Epot= -4.55118e+05 Fmax= 1.47622e+05, atom= 3297
> Step= 31, Dmax= 9.9e-02 nm, Epot= -4.84124e+05 Fmax= 8.03024e+04, atom= 3296
> Step= 32, Dmax= 1.2e-01 nm, Epot= -5.11472e+05 Fmax= 1.00688e+05, atom= 3296
> Wrote pdb files with previous and current coordinates
>
> -------------------------------------------------------
> Program gmx mdrun, VERSION 5.1.2
> Source code file: /build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/mdlib/constr.cpp, line: 555
>
> Fatal error:
>
> step 33: Water molecule starting at atom 39087 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
> How can I solve this problem?
>
You're starting from a really bad starting structure, apparently (note the
astronomical forces) and it is not relaxing well. How did you build the system?
How did you deal with the ligand? Have you investigated the environment
around the atoms experiencing high forces (the ones mdrun is printing out the
whole way)?
-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
==================================================
More information about the gromacs.org_gmx-users
mailing list