no daje "bash: ./gmx: Nie ma takiego pliku ani katalogu"
ale może ja nie mam całości potrzebnych plików,, bo po prostu mam w katalogu to co stąd ściągnięte
https://www.dropbox.com/s/v13w0x3z503d6j1/gmx-linux-cuda.zip i nic poza tym, może powinienme zacząć od przeczytania calego tego wątku
EDIT: chyba nie trzeba było nic innego ściągać. no w każdym razie nie hula
EDIT2: doinstalowałem gromacs-5.1-complete, zrobiłem PATH do plik gmx i wyszło tak:
[ja@komp gmx]$ sh start.sh
:-) GROMACS - gmx grompp, 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 grompp, VERSION 5.1.4
Executable: /usr/local/gromacs/gromacs-5.1.4//bin//gmx
Data prefix: /usr/local/gromacs/gromacs-5.1.4/
Command line:
gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr
Ignoring obsolete mdp entry 'title'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
Setting the LD random seed to 964890485
Generated 330891 of the 330891 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 330891 of the 330891 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'CL'
turning all bonds into constraints...
Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are: 209 Protein residues
There are: 12601 Water residues
There are: 4 Ion residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group Protein is 6565.76
Number of degrees of freedom in T-Coupling group non-Protein is 75615.24
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
Calculated rlist for 1x1 atom pair-list as 1.035 nm, buffer size 0.035 nm
Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
Reading Coordinates, Velocities and Box size from old trajectory
Will read whole trajectory
Last frame -1 time 100.000
Using frame at t = 100 ps
Starting time for run is 0 ps
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 48x48x48, spacing 0.154 0.154 0.154
Estimate for the relative computational load of the PME mesh part: 0.20
This run will generate roughly 1145 Mb of data
Back Off! I just backed up md_0_1.tpr to ./#md_0_1.tpr.1#
gcq#570: "This work contains many things which are new and interesting. Unfortunately, everything that is new is not interesting, and everything which is interesting, is not new." (Lev Landau)
:-) 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/gromacs-5.1.4//bin//gmx
Data prefix: /usr/local/gromacs/gromacs-5.1.4/
Command line:
gmx mdrun -nt 1 -gpu_id 0 -deffnm md_0_1
Back Off! I just backed up md_0_1.log to ./#md_0_1.log.1#
Running on 1 node with total 4 cores, 8 logical cores, 1 compatible GPU
Hardware detected:
CPU info:
Vendor: GenuineIntel
Brand: Intel(R) Xeon(R) CPU E3-1230 V2 @ 3.30GHz
SIMD instructions most likely to fit this hardware: AVX_256
SIMD instructions selected at GROMACS compile time: AVX_256
GPU info:
Number of GPUs detected: 1
#0: NVIDIA GeForce GTX 650, compute cap.: 3.0, ECC: no, stat: compatible
Reading file md_0_1.tpr, VERSION 5.1.4 (single precision)
Changing nstlist from 10 to 40, rlist from 1 to 1.097
Using 1 MPI thread
Using 1 OpenMP thread
1 GPU user-selected for this run.
Mapping of GPU ID to the 1 PP rank in this node: 0
Back Off! I just backed up md_0_1.trr to ./#md_0_1.trr.1#
Back Off! I just backed up md_0_1.xtc to ./#md_0_1.xtc.1#
Back Off! I just backed up md_0_1.edr to ./#md_0_1.edr.1#
starting mdrun 'Protein in water'
5000000 steps, 10000.0 ps.
^C
Received the INT signal, stopping at the next NS step
Core t (s) Wall t (s) (%)
Time: 499.293 452.751 110.3
(ns/day) (hour/ns)
Performance: 11.634 2.063
gcq#176: "Have a Nice Day" (R. McDonald)
Autor
Wątek: DrugDiscovery@Home (Przeczytany 63063 razy)