GROMACS 2018.8 2025-07-08T11:34:37.000 iram-ga-004815.extra.cea.fr 1 md-vv ; Velocity Verlet MD algorithm 0.002 ; Sets timestep at 2 fs 2500000 ; Sim will run 500,000 timesteps 500 ; Output to md.log every 500 dt 500 ; Output to ener.edr every 500 dt 500 ; Output to trajj.trr every 500 dt h-bonds ; Make H bonds in protein be rigid lincs ; Define algorithm to make bonds rigid Cut-off ; Define type of short-ranged interaction 0.875 ; Define short-ranged cutoff as 1 nm Verlet ; Generate pair lists to speed up simulation EnerPres ; Apply corrections to mitigate using cutoff xyz ; PBC in all 3 dimensions PME ; Define type of long-ranged interactions 0.875 ; Define long-ranged cutoff as 1nm 0.875 nose-hoover ; Define type of thermostat system ; Define groups to be affected by thermostat 300 ; Define temperature for each group in Kelvins 2.5 ; Define temperature coupling time 50 no ; Define type of barostat 1.0 ; Define system pressure in bars 2.0 ; Define pressure coupling time 1271 md-vv 0 0.002 2500000 0 1 Linear 100 0 1436594183 10 0.01 20 0 1000 10 0.05 500 0 0 500 100 500 0 1000 Verlet 10 Grid xyz false 0.005 0.875 PME Potential-shift 0 0.875 1 inf Cut-off Potential-shift 0 0.875 EnerPres 1 0.12 16 16 16 4 1e-05 0.001 Geometric 0 0 No Still 1 1 80 0 1 0.8 4.85 0.009 Ace-approximation 2.05016 Nose-Hoover 10 50 false No Isotropic -1 2 No 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 false 0 0 1 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 false no 0 0 0 0 0 0 0 0 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 300 2.5 No 0 0 0 0 N N N 18.014 18.014 18.014 90.0 90.0 90.0 2111.396299999998 GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof Aleksei Iupinov Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl 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) 2001-2017, 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. 21166.370 881.932 (ns/day) (hour/ns) 2025-07-08T11:49:19.000 Domain decomp.#DD comm. load#DD comm. bounds#Neighbor search#Comm. coord.#Force#Wait + Comm. F#PME mesh#NB X/F buffer ops.#Write traj.#Update#Constraints#Comm. energies#Rest 69.323 1.393 2.997 29.990 50.049 118.308 47.688 359.612 27.545 0.125 52.403 94.587 18.758 9.155 3485.680 70.062 150.687 1507.930 2516.542 5948.769 2397.838 18081.936 1385.010 6.302 2634.924 4755.992 943.182 460.322 7.9 0.2 0.3 3.4 5.7 13.4 5.4 40.8 3.1 0.0 5.9 10.7 2.1 1.0 881.932 44345.177 100.0 18.014 18.014 18.014 90.0 90.0 90.0 2111.396299999998 Bond 1.30329e+02 Angle 2.02245e+02 Ryckaert-Bell. 6.10011e+01 Improper Dih. 3.20677e+01 LJ-14 0.00000e+00 Coulomb-14 -6.26761e+03 LJ (SR) 9.05000e+02 Disper. corr. -1.77052e+02 Coulomb (SR) -1.13621e+04 Coul. recip. 1.02796e+02 Potential -1.63733e+04 Kinetic En. 1.58479e+03 Total Energy -1.47885e+04 Conserved En. -1.52112e+04 Temperature 2.99931e+02