[gmx-users] installation
David Sáez
davidsaezsan at gmail.com
Thu Feb 14 16:03:43 CET 2013
Thanks Justin, I'm gonna take your advice.
On Thu, Feb 14, 2013 at 11:43 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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*<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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
>
> --
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>
--
David A. Sáez San Martín
Químico-Farmacéutico
Concepción, Chile
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