# 'em.gro' does not exist **URL:** \ **Category:** User discussions\ **Created:** [November 8, 2021, 9:51pm UTC](https://gromacs.bioexcel.eu/t/em-gro-does-not-exist/3106 "2021-11-08T21:51:58Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![Somaia](https://avatars.discourse-cdn.com/v4/letter/s/35a633/32.png) [@Somaia](https://gromacs.bioexcel.eu/u/Somaia)\ **Post date:** [November 8, 2021, 9:51pm UTC](https://gromacs.bioexcel.eu/t/em-gro-does-not-exist/3106/1 "2021-11-08T21:51:58Z")
GROMACS version:2020.3 GROMACS modification: Yes/No I am doing molecular dynamic simulation for a ligand-protein complex. I have followed the steps in the GROMACS tutorial and used the em.mpd file in the tutorial for energy minimization parameters. However, the following error message appeared: Error in user input: Invalid command-line options In command-line option -f File ‘em.gro’ does not exist or is not accessible. The file could not be opened. Reason: No such file or directory (call to fopen() returned error code 2) I have recently realized that this error emerged due to failure or incomplete energy minimization, but I do not know how to fix it. Any suggetsion? ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [November 9, 2021, 2:38am UTC](https://gromacs.bioexcel.eu/t/em-gro-does-not-exist/3106/2 "2021-11-09T02:38:16Z")
> [@Somaia](#): > > I have recently realized that this error emerged due to failure or incomplete energy minimization, but I do not know how to fix it. Any suggetsion? Not without substantially more information. What happened during minimization, what was the outcome in terms of Fmax? What is in your system and how did you build it? Do you have any non-standard species that you’ve parametrized yourself? ---
**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\ **Post date:** [November 9, 2021, 7:55pm UTC](https://gromacs.bioexcel.eu/t/em-gro-does-not-exist/3106/3 "2021-11-09T19:55:21Z")
Paste your energy minimisations log file. The minimisation is not completed and \*.gro file is not generated. ---
**Author:** ![Somaia](https://avatars.discourse-cdn.com/v4/letter/s/35a633/32.png) [@Somaia](https://gromacs.bioexcel.eu/u/Somaia)\ **Post date:** [November 9, 2021, 8:27pm UTC](https://gromacs.bioexcel.eu/t/em-gro-does-not-exist/3106/4 "2021-11-09T20:27:42Z")
``` :-) GROMACS - gmx mdrun, 2020.3 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd ``` Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf Artem Zhmurov 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) 2001-2019, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out [http://www.gromacs.org](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 2020.3 Executable: /usr/local/bin/gmx Data prefix: /usr/local Working dir: /mnt/e/WKMD Process ID: 83 Command line: gmx mdrun -v -deffnm em GROMACS version: 2020.3 Verified release checksum is c0599e547549c2d0ef4fc678dc5a26ad0000eab045e938fed756f9ff5b99a197 Precision: single Memory model: 64 bit MPI library: thread\_mpi OpenMP support: enabled (GMX\_OPENMP\_MAX\_THREADS = 64) GPU support: disabled SIMD instructions: AVX2\_256 FFT library: fftw-3.3.8-sse2-avx-avx2-avx2\_128 RDTSCP usage: enabled TNG support: enabled Hwloc support: disabled Tracing support: disabled C compiler: /usr/bin/cc GNU 9.3.0 C compiler flags: -mavx2 -mfma -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG C++ compiler: /usr/bin/c++ GNU 9.3.0 C++ compiler flags: -mavx2 -mfma -fexcess-precision=fast -funroll-all-loops -fopenmp Running on 1 node with total 12 cores, 12 logical cores Hardware detected: CPU info: Vendor: Intel Brand: Intel(R) Core™ i7-9750H CPU @ 2.60GHz Family: 6 Model: 158 Stepping: 10 Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop\_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic Hardware topology: Only logical processor count ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E. Lindahl GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers SoftwareX 1 (2015) pp. 19-25 -------- -------- — Thank You — -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27 -------- -------- — Thank You — -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit Bioinformatics 29 (2013) pp. 845-54 -------- -------- — Thank You — -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 435-447 -------- -------- — Thank You — -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen GROMACS: Fast, Flexible and Free J. Comp. Chem. 26 (2005) pp. 1701-1719 -------- -------- — Thank You — -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ E. Lindahl and B. Hess and D. van der Spoel GROMACS 3.0: A package for molecular simulation and trajectory analysis J. Mol. Mod. 7 (2001) pp. 306-317 -------- -------- — Thank You — -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ H. J. C. Berendsen, D. van der Spoel and R. van Drunen GROMACS: A message-passing parallel molecular dynamics implementation Comp. Phys. Comm. 91 (1995) pp. 43-56 -------- -------- — Thank You — -------- -------- ++++ PLEASE CITE THE DOI FOR THIS VERSION OF GROMACS ++++ > **[GROMACS 2020.3 Source code](https://zenodo.org/record/3923645)** > > Source code archive of the 2020.3 version of GROMACS. -------- -------- — Thank You — -------- -------- Input Parameters: integrator = steep tinit = 0 dt = 0.001 nsteps = 50000 init-step = 0 simulation-part = 1 comm-mode = Linear nstcomm = 100 bd-fric = 0 ld-seed = 1278885625 emtol = 1000 emstep = 0.01 niter = 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr = 10 rtpi = 0.05 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstcalcenergy = 100 nstenergy = 1000 nstxout-compressed = 0 compressed-x-precision = 1000 cutoff-scheme = Verlet nstlist = 10 pbc = xyz periodic-molecules = false verlet-buffer-tolerance = 0.005 rlist = 1.26 coulombtype = PME coulomb-modifier = Potential-shift rcoulomb-switch = 0 rcoulomb = 1.2 epsilon-r = 1 epsilon-rf = inf vdw-type = Cut-off vdw-modifier = Force-switch rvdw-switch = 1 rvdw = 1.2 DispCorr = No table-extension = 1 fourierspacing = 0.12 fourier-nx = 96 fourier-ny = 96 fourier-nz = 96 pme-order = 4 ewald-rtol = 1e-05 ewald-rtol-lj = 0.001 lj-pme-comb-rule = Geometric ewald-geometry = 0 epsilon-surface = 0 tcoupl = No nsttcouple = -1 nh-chain-length = 0 print-nose-hoover-chain-variables = false pcoupl = No pcoupltype = Isotropic nstpcouple = -1 tau-p = 1 compressibility (3x3): compressibility[0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compressibility[1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compressibility[2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref-p (3x3): ref-p[0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref-p[1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref-p[2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} refcoord-scaling = No posres-com (3): posres-com[0]= 0.00000e+00 posres-com[1]= 0.00000e+00 posres-com[2]= 0.00000e+00 posres-comB (3): posres-comB[0]= 0.00000e+00 posres-comB[1]= 0.00000e+00 posres-comB[2]= 0.00000e+00 QMMM = false QMconstraints = 0 QMMMscheme = 0 MMChargeScaleFactor = 1 qm-opts: ngQM = 0 constraint-algorithm = Lincs continuation = false Shake-SOR = false shake-tol = 0.0001 lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 nwall = 0 wall-type = 9-3 wall-r-linpot = -1 wall-atomtype[0] = -1 wall-atomtype[1] = -1 wall-density[0] = 0 wall-density[1] = 0 wall-ewald-zfac = 3 pull = false awh = false rotation = false interactiveMD = false disre = No disre-weighting = Conservative disre-mixed = false dr-fc = 1000 dr-tau = 0 nstdisreout = 100 orire-fc = 0 orire-tau = 0 nstorireout = 100 free-energy = no cos-acceleration = 0 deform (3x3): deform[0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} deform[1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} deform[2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} simulated-tempering = false swapcoords = no userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0 applied-forces: electric-field: x: E0 = 0 omega = 0 t0 = 0 sigma = 0 y: E0 = 0 omega = 0 t0 = 0 sigma = 0 z: E0 = 0 omega = 0 t0 = 0 sigma = 0 density-guided-simulation: active = false group = protein similarity-measure = inner-product atom-spreading-weight = unity force-constant = 1e+09 gaussian-transform-spreading-width = 0.2 gaussian-transform-spreading-range-in-multiples-of-width = 4 reference-density-filename = reference.mrc nst = 1 normalize-densities = true adaptive-force-scaling = false adaptive-force-scaling-time-constant = 4 grpopts: nrdf: 200826 ref-t: 0 tau-t: 0 annealing: No annealing-npoints: 0 acc: 0 0 0 nfreeze: N N N energygrp-flags[0]: 0 Using 1 MPI thread Non-default thread affinity set, disabling internal thread affinity Using 12 OpenMP threads System total charge: 0.000 Will do PME sum in reciprocal space for electrostatic interactions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen A smooth particle mesh Ewald method J. Chem. Phys. 103 (1995) pp. 8577-8592 -------- -------- — Thank You — -------- -------- Using a Gaussian width (1/beta) of 0.384195 nm for Ewald Potential shift: LJ r^-12: -2.648e-01 r^-6: -5.349e-01, Ewald -8.333e-06 Initialized non-bonded Ewald tables, spacing: 1.02e-03 size: 1176 Generated table with 1130 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1130 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1130 data points for 1-4 LJ12. Tabscale = 500 points/nm Using SIMD 4x8 nonbonded short-range kernels Using a 4x8 pair-list setup: updated every 10 steps, buffer 0.060 nm, rlist 1.260 nm Removing pbc first time ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ S. Miyamoto and P. A. Kollman SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid Water Models J. Comp. Chem. 13 (1992) pp. 952-962 -------- -------- — Thank You — -------- -------- ---
**Author:** ![Somaia](https://avatars.discourse-cdn.com/v4/letter/s/35a633/32.png) [@Somaia](https://gromacs.bioexcel.eu/u/Somaia)\ **Post date:** [November 9, 2021, 8:37pm UTC](https://gromacs.bioexcel.eu/t/em-gro-does-not-exist/3106/5 "2021-11-09T20:37:35Z")
I am completely new to GROMACS. I do not know where I can find the data you are asking about. I have followed the steps illustrated in GROMACS official tutorial precisely. My ligand was parametrized using CGenFF. ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [November 12, 2021, 2:22am UTC](https://gromacs.bioexcel.eu/t/em-gro-does-not-exist/3106/6 "2021-11-12T02:22:33Z")
Energy minimization never even started. Did you get any kind of error printed to the terminal? What happens when you run in verbose mode (`mdrun -v`)? Can you minimize the protein alone, and the ligand alone (in vacuum and in solution)? Troubleshooting tips for protein-ligand complexes are given at [Terminology — GROMACS 2021.4 documentation](https://manual.gromacs.org/current/user-guide/terminology.html#diagnosing-an-unstable-system)