<p dir="ltr">Hi,</p>
<p dir="ltr">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!</p>
<p dir="ltr">Matk</p>
<br><div class="gmail_quote"><div dir="ltr">On Wed, 18 Oct 2017 19:23 Robert Nairn <<a href="mailto:rn33@st-andrews.ac.uk">rn33@st-andrews.ac.uk</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div><div>Dear all, <br><br></div>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. <br><br><br>[christos@chpc-cp39 Simulation]$ gmx mdrun -v -deffnm em<br> :-) GROMACS - gmx mdrun, VERSION 5.1.4 (-:<br><br> GROMACS is written by:<br> Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar <br> Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch <br> Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen<br> Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner <br> Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff <br> Erik Marklund Teemu Murtola Szilard Pall Sander Pronk <br> Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers <br> Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf <br> and the project leaders:<br> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel<br><br>Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br>Copyright (c) 2001-2015, The GROMACS development team at<br>Uppsala University, Stockholm University and<br>the Royal Institute of Technology, Sweden.<br>check out <a href="http://www.gromacs.org" target="_blank">http://www.gromacs.org</a> for more information.<br><br>GROMACS is free software; you can redistribute it and/or modify it<br>under the terms of the GNU Lesser General Public License<br>as published by the Free Software Foundation; either version 2.1<br>of the License, or (at your option) any later version.<br><br>GROMACS: gmx mdrun, VERSION 5.1.4<br>Executable: /usr/local/gromacs/bin/gmx<br>Data prefix: /usr/local/gromacs<br>Command line:<br> gmx mdrun -v -deffnm em<br><br><br>Back Off! I just backed up em.log to ./#em.log.7#<br><br>Running on 1 node with total 4 cores, 4 logical cores<br>Hardware detected:<br> CPU info:<br> Vendor: GenuineIntel<br> Brand: Intel(R) Core(TM) i5-4460 CPU @ 3.20GHz<br> SIMD instructions most likely to fit this hardware: AVX2_256<br> SIMD instructions selected at GROMACS compile time: AVX2_256<br><br>Reading file em.tpr, VERSION 5.1.4 (single precision)<br>Using 1 MPI thread<br>Using 4 OpenMP threads <br><br><br>Back Off! I just backed up em.trr to ./#em.trr.7#<br><br>Back Off! I just backed up em.edr to ./#em.edr.7#<br><br>Steepest Descents:<br> Tolerance (Fmax) = 1.00000e+03<br> Number of steps = 50000<br>Step= 0, Dmax= 1.0e-02 nm, Epot= -3.20786e+05 Fmax= 1.71766e+03, atom= 328<br>Step= 2, Dmax= 5.0e-03 nm, Epot= -3.22206e+05 Fmax= 2.42847e+03, atom= 5581<br>Step= 3, Dmax= 6.0e-03 nm, Epot= -3.22537e+05 Fmax= 5.33224e+03, atom= 5581<br>Step= 4, Dmax= 7.2e-03 nm, Epot= -3.23803e+05 Fmax= 3.73628e+03, atom= 5581<br>Step= 6, Dmax= 4.3e-03 nm, Epot= -3.24377e+05 Fmax= 1.77965e+03, atom= 5581<br>Step= 7, Dmax= 5.2e-03 nm, Epot= -3.24696e+05 Fmax= 4.72325e+03, atom= 5581<br>Step= 8, Dmax= 6.2e-03 nm, Epot= -3.25203e+05 Fmax= 3.21307e+03, atom= 5581<br>Step= 10, Dmax= 3.7e-03 nm, Epot= -3.25578e+05 Fmax= 1.53786e+03, atom= 5581<br>Step= 11, Dmax= 4.5e-03 nm, Epot= -3.25794e+05 Fmax= 4.19745e+03, atom= 5581<br>Step= 12, Dmax= 5.4e-03 nm, Epot= -3.26199e+05 Fmax= 2.65229e+03, atom= 5581<br>Step= 14, Dmax= 3.2e-03 nm, Epot= -3.26475e+05 Fmax= 1.44458e+03, atom= 5581<br>Step= 15, Dmax= 3.9e-03 nm, Epot= -3.26646e+05 Fmax= 3.51711e+03, atom= 889<br>Step= 16, Dmax= 4.6e-03 nm, Epot= -3.26945e+05 Fmax= 2.42357e+03, atom= 889<br>Step= 18, Dmax= 2.8e-03 nm, Epot= -3.27174e+05 Fmax= 1.16101e+03, atom= 889<br>Step= 19, Dmax= 3.3e-03 nm, Epot= -3.27357e+05 Fmax= 3.10626e+03, atom= 889<br>Step= 20, Dmax= 4.0e-03 nm, Epot= -3.27599e+05 Fmax= 2.04763e+03, atom= 889<br>Step= 21, Dmax= 4.8e-03 nm, Epot= -3.27618e+05 Fmax= 4.11224e+03, atom= 889<br>Step= 22, Dmax= 5.8e-03 nm, Epot= -3.27866e+05 Fmax= 3.29947e+03, atom= 889<br>Step= 24, Dmax= 3.5e-03 nm, Epot= -3.28131e+05 Fmax= 1.11942e+03, atom= 889<br>Step= 25, Dmax= 4.2e-03 nm, Epot= -3.28185e+05 Fmax= 4.23073e+03, atom= 889<br>Step= 26, Dmax= 5.0e-03 nm, Epot= -3.28509e+05 Fmax= 2.13723e+03, atom= 889<br>Step= 28, Dmax= 3.0e-03 nm, Epot= -3.28653e+05 Fmax= 1.71455e+03, atom= 889<br>Step= 29, Dmax= 3.6e-03 nm, Epot= -3.28732e+05 Fmax= 2.86474e+03, atom= 889<br>Step= 30, Dmax= 4.3e-03 nm, Epot= -3.28867e+05 Fmax= 2.67060e+03, atom= 889<br>Step= 31, Dmax= 5.2e-03 nm, Epot= -3.28877e+05 Fmax= 3.93851e+03, atom= 889<br>Step= 32, Dmax= 6.2e-03 nm, Epot= -3.28983e+05 Fmax= 4.01820e+03, atom= 889<br>Step= 34, Dmax= 3.7e-03 nm, Epot= -3.29290e+05 Fmax= 7.22653e+02, atom= 889<br><br>writing lowest energy coordinates.<br><br>Back Off! I just backed up em.gro to ./#em.gro.7#<br><br>Steepest Descents converged to Fmax < 1000 in 35 steps<br>Potential Energy = -3.2929012e+05<br>Maximum force = 7.2265314e+02 on atom 889<br>Norm of force = 7.2922180e+01<br><br>NOTE: 20 % of the run time was spent in pair search,<br> you might want to increase nstlist (this has no effect on accuracy)<br><br><br>gcq#490: "I have a hunch that the unknown sequences of DNA will decode into copyright notices and patent protections." (Donald Knuth)<br><br>[christos@chpc-cp39 Simulation]$ perl <a href="http://inflategro.pl" target="_blank">inflategro.pl</a> em.gro 0.95 DMPC 0 system_shrink1.gro 5 area_shrink1.dat<br>Reading..... <br>Scaling lipids....<br>There are 128 lipids...<br>with 46 atoms per lipid..<br><br>Determining upper and lower leaflet...<br>64 lipids in the upper...<br>64 lipids in the lower leaflet <br><br>No protein coordinates found...<br>Writing scaled bilayer & centered protein...<br><br><br>Calculating Area per lipid...<br>Protein X-min/max: 10000 -9999<br>Protein Y-min/max: 10000 -9999<br>X-range: -19999 A Y-range: -19999 A<br>Building -19999 X -19999 2D grid on protein coordinates...<br>Calculating area occupied by protein..<br>full TMD..<br>upper TMD..<br>lower TMD..<br>Area per protein: 0 nm^2<br>Area per lipid: 0.53787556 nm^2<br><br>Area per protein, upper half: 0 nm^2<br>Area per lipid, upper leaflet : 0.53787556 nm^2<br><br>Area per protein, lower half: 0 nm^2<br>Area per lipid, lower leaflet : 0.53787556 nm^2<br><br>Writing Area per lipid...<br>Done!<br><br></div>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. <br><br></div>Best, <br><br></div>Robert <br><div><div><div><br><br></div></div></div></div>
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