[gmx-users] Water molecule starting at atom 39087 can not be settled
liming_52
liming_52 at 163.com
Wed Mar 22 00:08:20 CET 2017
The position of the ligand was obtained using autodock vina. The gro file and ITP file were obtained from the PRODRG server (http://davapc1.bioch.dundee.ac.uk/prodrg). Anyway, I added the ions with 0.154 M NaCl. Did these effect my md?
--
With my best wishes,
Ming Li, PhD
Chinese Academy of Agricultural Sciences, Beijing, China
At 2017-03-22 06:53:57, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>
>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
>
>==================================================
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