[gmx-users] installation
Justin Lemkul
jalemkul at vt.edu
Thu Feb 14 15:43:53 CET 2013
On 2/14/13 9:40 AM, David Sáez wrote:
> Erik, thanks for your answer. I typed "which mdrun" and I got this output:
>
> *~$ which mdrun*
> */usr/local/gromacs/bin/mdrun*
>
> Then, I typed just "mdrun" and I got this:
>
>
> *~$ mdrun*
> * *
> * :-) G R O M A C S (-:*
> *
> *
> * Green Red Orange Magenta Azure Cyan Skyblue*
> *
> *
> * :-) VERSION 4.6 (-:*
> *
> *
> * Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, *
> * Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, *
> * Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,
> *
> * Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, *
> * Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, *
> * Michael Shirts, Alfons Sijbers, Peter Tieleman,*
> *
> *
> * Berk Hess, David van der Spoel, and Erik Lindahl.*
> *
> *
> * Copyright (c) 1991-2000, University of Groningen, The Netherlands.*
> * Copyright (c) 2001-2012,2013, The GROMACS development team at*
> * Uppsala University & The Royal Institute of Technology, Sweden.*
> * check out http://www.gromacs.org for more information.*
> *
> *
> * This program 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.*
> *
> *
> * :-) mdrun (-:*
> *
> *
> *Option Filename Type Description*
> *------------------------------------------------------------*
> * -s topol.tpr Input Run input file: tpr tpb tpa*
> * -o traj.trr Output Full precision trajectory: trr trj cpt*
> * -x traj.xtc Output, Opt. Compressed trajectory (portable xdr
> format)*
> *-cpi state.cpt Input, Opt. Checkpoint file*
> *-cpo state.cpt Output, Opt. Checkpoint file*
> * -c confout.gro Output Structure file: gro g96 pdb etc.*
> * -e ener.edr Output Energy file*
> * -g md.log Output Log file*
> *-dhdl dhdl.xvg Output, Opt. xvgr/xmgr file*
> *-field field.xvg Output, Opt. xvgr/xmgr file*
> *-table table.xvg Input, Opt. xvgr/xmgr file*
> *-tabletf tabletf.xvg Input, Opt. xvgr/xmgr file*
> *-tablep tablep.xvg Input, Opt. xvgr/xmgr file*
> *-tableb table.xvg Input, Opt. xvgr/xmgr file*
> *-rerun rerun.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt*
> *-tpi tpi.xvg Output, Opt. xvgr/xmgr file*
> *-tpid tpidist.xvg Output, Opt. xvgr/xmgr file*
> * -ei sam.edi Input, Opt. ED sampling input*
> * -eo edsam.xvg Output, Opt. xvgr/xmgr file*
> * -j wham.gct Input, Opt. General coupling stuff*
> * -jo bam.gct Output, Opt. General coupling stuff*
> *-ffout gct.xvg Output, Opt. xvgr/xmgr file*
> *-devout deviatie.xvg Output, Opt. xvgr/xmgr file*
> *-runav runaver.xvg Output, Opt. xvgr/xmgr file*
> * -px pullx.xvg Output, Opt. xvgr/xmgr file*
> * -pf pullf.xvg Output, Opt. xvgr/xmgr file*
> * -ro rotation.xvg Output, Opt. xvgr/xmgr file*
> * -ra rotangles.log Output, Opt. Log file*
> * -rs rotslabs.log Output, Opt. Log file*
> * -rt rottorque.log Output, Opt. Log file*
> *-mtx nm.mtx Output, Opt. Hessian matrix*
> * -dn dipole.ndx Output, Opt. Index file*
> *-multidir rundir Input, Opt., Mult. Run directory*
> *-membed membed.dat Input, Opt. Generic data file*
> * -mp membed.top Input, Opt. Topology file*
> * -mn membed.ndx Input, Opt. Index file*
> *
> *
> *Option Type Value Description*
> *------------------------------------------------------*
> *-[no]h bool no Print help info and quit*
> *-[no]version bool no Print version info and quit*
> *-nice int 0 Set the nicelevel*
> *-deffnm string Set the default filename for all file options*
> *-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none*
> *-[no]pd bool no Use particle decompostion*
> *-dd vector 0 0 0 Domain decomposition grid, 0 is optimize*
> *-ddorder enum interleave DD node order: interleave, pp_pme or
> cartesian*
> *-npme int -1 Number of separate nodes to be used for PME, -1
> *
> * is guess*
> *-nt int 0 Total number of threads to start (0 is guess)*
> *-ntmpi int 0 Number of thread-MPI threads to start (0 is
> guess)*
> *-ntomp int 0 Number of OpenMP threads per MPI process/thread
> *
> * to start (0 is guess)*
> *-ntomp_pme int 0 Number of OpenMP threads per MPI process/thread
> *
> * to start (0 is -ntomp)*
> *-pin enum auto Fix threads (or processes) to specific cores:*
> * auto, on or off*
> *-pinoffset int 0 The starting logical core number for pinning to
> *
> * cores; used to avoid pinning threads from*
> * different mdrun instances to the same core*
> *-pinstride int 0 Pinning distance in logical cores for threads,*
> * use 0 to minimize the number of threads per*
> * physical core*
> *-gpu_id string List of GPU id's to use*
> *-[no]ddcheck bool yes Check for all bonded interactions with DD*
> *-rdd real 0 The maximum distance for bonded interactions
> with*
> * DD (nm), 0 is determine from initial
> coordinates*
> *-rcon real 0 Maximum distance for P-LINCS (nm), 0 is
> estimate*
> *-dlb enum auto Dynamic load balancing (with DD): auto, no or
> yes*
> *-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
> *
> *-gcom int -1 Global communication frequency*
> *-nb enum auto Calculate non-bonded interactions on: auto,
> cpu,*
> * gpu or gpu_cpu*
> *-[no]tunepme bool yes Optimize PME load between PP/PME nodes or
> GPU/CPU*
> *-[no]testverlet bool no Test the Verlet non-bonded scheme*
> *-[no]v bool no Be loud and noisy*
> *-[no]compact bool yes Write a compact log file*
> *-[no]seppot bool no Write separate V and dVdl terms for each*
> * interaction type and node to the log file(s)*
> *-pforce real -1 Print all forces larger than this (kJ/mol nm)*
> *-[no]reprod bool no Try to avoid optimizations that affect binary*
> * reproducibility*
> *-cpt real 15 Checkpoint interval (minutes)*
> *-[no]cpnum bool no Keep and number checkpoint files*
> *-[no]append bool yes Append to previous output files when continuing
> *
> * from checkpoint instead of adding the
> simulation*
> * part number to all file names*
> *-nsteps int -2 Run this number of steps, overrides .mdp file*
> * option*
> *-maxh real -1 Terminate after 0.99 times this time (hours)*
> *-multi int 0 Do multiple simulations in parallel*
> *-replex int 0 Attempt replica exchange periodically with this
> *
> * period (steps)*
> *-nex int 0 Number of random exchanges to carry out each*
> * exchange interval (N^3 is one suggestion).
> -nex*
> * zero or not specified gives neighbor replica*
> * exchange.*
> *-reseed int -1 Seed for replica exchange, -1 is generate a
> seed*
> *-[no]ionize bool no Do a simulation including the effect of an
> X-Ray*
> * bombardment on your system*
> *
> *
> *
> *
> *Back Off! I just backed up md.log to ./#md.log.6#*
> *
> *
> *-------------------------------------------------------*
> *Program mdrun, VERSION 4.6*
> *Source code file: /home/david/Descargas/gromacs-4.6/src/gmxlib/gmxfio.c,
> line: 524*
> *
> *
> *Can not open file:*
> *topol.tpr*
> *For more information and tips for troubleshooting, please check the GROMACS
> *
> *website at http://www.gromacs.org/Documentation/Errors*
> *-------------------------------------------------------*
> *
> *
> *"If I Were You I Would Give Me a Break" (F. Black)*
> *
> *
> As you can see, there is a problem with topol.tpr, I tried* to find it
> manually, but it is not in the computer's hard disk.*
> *
> *
> *Thanks in advance.*
>
All Gromacs programs have default file names that they use if you don't specify
them otherwise (note that they're all listed in the above screen output). mdrun
requires a .tpr file as input to tell it what to do. You didn't give an
explicit file name for it to use, so it tried to use the default, which doesn't
exist. Please do some basic tutorial material to familiarize yourself with a
proper workflow and normal command usage.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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