[gmx-users] (no subject)

Justin Lemkul jalemkul at vt.edu
Thu Oct 19 16:55:36 CEST 2017 


On 10/19/17 8:04 AM, Robert Nairn wrote:
> Dear all,
>
> I am currently trying to insert the MscL protein into the DMPC bilayer. I
> followed Justin Lemkul's tutorial 2 (with the exception of using dmpc
> instead of dppc) and receive this error message after shrinking and energy
> minimization.
>
>
> [christos at chpc-cp39 Simulation]$ gmx mdrun -v -deffnm em
>                     :-) GROMACS - gmx mdrun, VERSION 5.1.4 (-:
>
>                              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 5.1.4
> Executable:   /usr/local/gromacs/bin/gmx
> Data prefix:  /usr/local/gromacs
> Command line:
>    gmx mdrun -v -deffnm em
>
>
> Back Off! I just backed up em.log to ./#em.log.7#
>
> Running on 1 node with total 4 cores, 4 logical cores
> Hardware detected:
>    CPU info:
>      Vendor: GenuineIntel
>      Brand:  Intel(R) Core(TM) i5-4460  CPU @ 3.20GHz
>      SIMD instructions most likely to fit this hardware: AVX2_256
>      SIMD instructions selected at GROMACS compile time: AVX2_256
>
> Reading file em.tpr, VERSION 5.1.4 (single precision)
> Using 1 MPI thread
> Using 4 OpenMP threads
>
>
> Back Off! I just backed up em.trr to ./#em.trr.7#
>
> Back Off! I just backed up em.edr to ./#em.edr.7#
>
> Steepest Descents:
>     Tolerance (Fmax)   =  1.00000e+03
>     Number of steps    =        50000
> Step=    0, Dmax= 1.0e-02 nm, Epot= -3.20786e+05 Fmax= 1.71766e+03, atom=
> 328
> Step=    2, Dmax= 5.0e-03 nm, Epot= -3.22206e+05 Fmax= 2.42847e+03, atom=
> 5581
> Step=    3, Dmax= 6.0e-03 nm, Epot= -3.22537e+05 Fmax= 5.33224e+03, atom=
> 5581
> Step=    4, Dmax= 7.2e-03 nm, Epot= -3.23803e+05 Fmax= 3.73628e+03, atom=
> 5581
> Step=    6, Dmax= 4.3e-03 nm, Epot= -3.24377e+05 Fmax= 1.77965e+03, atom=
> 5581
> Step=    7, Dmax= 5.2e-03 nm, Epot= -3.24696e+05 Fmax= 4.72325e+03, atom=
> 5581
> Step=    8, Dmax= 6.2e-03 nm, Epot= -3.25203e+05 Fmax= 3.21307e+03, atom=
> 5581
> Step=   10, Dmax= 3.7e-03 nm, Epot= -3.25578e+05 Fmax= 1.53786e+03, atom=
> 5581
> Step=   11, Dmax= 4.5e-03 nm, Epot= -3.25794e+05 Fmax= 4.19745e+03, atom=
> 5581
> Step=   12, Dmax= 5.4e-03 nm, Epot= -3.26199e+05 Fmax= 2.65229e+03, atom=
> 5581
> Step=   14, Dmax= 3.2e-03 nm, Epot= -3.26475e+05 Fmax= 1.44458e+03, atom=
> 5581
> Step=   15, Dmax= 3.9e-03 nm, Epot= -3.26646e+05 Fmax= 3.51711e+03, atom=
> 889
> Step=   16, Dmax= 4.6e-03 nm, Epot= -3.26945e+05 Fmax= 2.42357e+03, atom=
> 889
> Step=   18, Dmax= 2.8e-03 nm, Epot= -3.27174e+05 Fmax= 1.16101e+03, atom=
> 889
> Step=   19, Dmax= 3.3e-03 nm, Epot= -3.27357e+05 Fmax= 3.10626e+03, atom=
> 889
> Step=   20, Dmax= 4.0e-03 nm, Epot= -3.27599e+05 Fmax= 2.04763e+03, atom=
> 889
> Step=   21, Dmax= 4.8e-03 nm, Epot= -3.27618e+05 Fmax= 4.11224e+03, atom=
> 889
> Step=   22, Dmax= 5.8e-03 nm, Epot= -3.27866e+05 Fmax= 3.29947e+03, atom=
> 889
> Step=   24, Dmax= 3.5e-03 nm, Epot= -3.28131e+05 Fmax= 1.11942e+03, atom=
> 889
> Step=   25, Dmax= 4.2e-03 nm, Epot= -3.28185e+05 Fmax= 4.23073e+03, atom=
> 889
> Step=   26, Dmax= 5.0e-03 nm, Epot= -3.28509e+05 Fmax= 2.13723e+03, atom=
> 889
> Step=   28, Dmax= 3.0e-03 nm, Epot= -3.28653e+05 Fmax= 1.71455e+03, atom=
> 889
> Step=   29, Dmax= 3.6e-03 nm, Epot= -3.28732e+05 Fmax= 2.86474e+03, atom=
> 889
> Step=   30, Dmax= 4.3e-03 nm, Epot= -3.28867e+05 Fmax= 2.67060e+03, atom=
> 889
> Step=   31, Dmax= 5.2e-03 nm, Epot= -3.28877e+05 Fmax= 3.93851e+03, atom=
> 889
> Step=   32, Dmax= 6.2e-03 nm, Epot= -3.28983e+05 Fmax= 4.01820e+03, atom=
> 889
> Step=   34, Dmax= 3.7e-03 nm, Epot= -3.29290e+05 Fmax= 7.22653e+02, atom=
> 889
>
> writing lowest energy coordinates.
>
> Back Off! I just backed up em.gro to ./#em.gro.7#
>
> Steepest Descents converged to Fmax < 1000 in 35 steps
> Potential Energy  = -3.2929012e+05
> Maximum force     =  7.2265314e+02 on atom 889
> Norm of force     =  7.2922180e+01
>
> NOTE: 20 % of the run time was spent in pair search,
>        you might want to increase nstlist (this has no effect on accuracy)
>
>
> gcq#490: "I have a hunch that the unknown sequences of DNA will decode into
> copyright notices and patent protections." (Donald Knuth)
>
> [christos at chpc-cp39 Simulation]$ perl inflategro.pl em.gro 0.95 DMPC 0
> system_shrink1.gro 5 area_shrink1.dat
> Reading.....
> Scaling lipids....
> There are 128 lipids...
> with 46 atoms per lipid..
>
> Determining upper and lower leaflet...
> 64 lipids in the upper...
> 64 lipids in the lower leaflet
>
> No protein coordinates found...

This line is key - make sure you have what you think you have (e.g. you 
didn't accidentally just minimize a bilayer with no protein or something).

-Justin

> Writing scaled bilayer & centered protein...
>
>
> Calculating Area per lipid...
> Protein X-min/max: 10000    -9999
> Protein Y-min/max: 10000    -9999
> X-range: -19999 A    Y-range: -19999 A
> Building -19999 X -19999 2D grid on protein coordinates...
> Calculating area occupied by protein..
> full TMD..
> upper TMD..
> lower TMD..
> Area per protein: 0 nm^2
> Area per lipid: 0.53787556 nm^2
>
> Area per protein, upper half: 0 nm^2
> Area per lipid, upper leaflet : 0.53787556 nm^2
>
> Area per protein, lower half: 0 nm^2
> Area per lipid, lower leaflet : 0.53787556 nm^2
>
> Writing Area per lipid...
> Done!
>
> I've also tried the same process with popc and dppc and get the same error
> message. I've previously read that it could be an issue with the grompp
> coordinate input file, but I'm not sure what is wrong in this instance.
>
> Best,
>
> Robert

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================

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