[gmx-developers] Problem inserting protein to membrane during InflateGro
Mark Abraham
mark.j.abraham at gmail.com
Wed Oct 18 20:18:35 CEST 2017
Hi,
This mailing list is for questions pertaining to GROMACS development. I see
an error from inflategro, but since that is not a GROMACS tool, the users
list or its support forum might be more useful to you!
Matk
On Wed, 18 Oct 2017 19:23 Robert Nairn <rn33 at st-andrews.ac.uk> 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...
> 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
>
>
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