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.* On Wed, Feb 13, 2013 at 5:50 AM, Erik Marklund <er...@xray.bmc.uu.se> wrote: > It shouldn't generate output. It will make your system find your gromacs > installation, however. Try e.g. "which mdrun". > > Erik > > > On Feb 13, 2013, at 5:06 AM, David Sáez wrote: > > Thanks for your answer Justin. I followed your advice: >> When I type >> *$ source /usr/local/gromacs/bin/GMXRC* >> *$* >> >> >> Nothing happened, the prompt returns normally and no action is executed. >> Do >> you have any idea? >> >> >> On Tue, Feb 12, 2013 at 11:27 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 2/12/13 9:24 PM, David Sáez wrote: >>> >>> Hello everybody, I'm trying to install Gromacs 4.6 in my Ubuntu 12.04 >>>> laptop. As I am not a a skilled user, I tried the Quick and Dirty >>>> Installation, After following the instructions I obtained this message >>>> when >>>> trying to execute GMXRC: >>>> >>>> david@HAL-9000:~$ /usr/local/gromacs/bin/GMXRC >>>> /usr/local/gromacs/bin/GMXRC: line 34: return: can only `return' from a >>>> function or sourced script >>>> /usr/local/gromacs/bin/GMXRC: line 43: CSH:: command not found >>>> /usr/local/gromacs/bin/GMXRC.****csh: line 8: syntax error near >>>> unexpected >>>> token `setenv' >>>> /usr/local/gromacs/bin/GMXRC.****csh: line 8: `if (! $?LD_LIBRARY_PATH) >>>> >>>> setenv >>>> LD_LIBRARY_PATH ""' >>>> >>>> Could someone give some help? >>>> >>>> >>>> Note the first error - you need to source the file. >>> >>> $ source /usr/local/gromacs/bin/GMXRC >>> >>> -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://vt.edu/Pages/Personal/justin> >>> <h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >>> > >>> >>> ==============================****========== >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> > >>> * Please search the archive at http://www.gromacs.org/** >>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/** >>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>before >>> posting! >>> >>> * Please don't post (un)subscribe requests to the list. Use the www >>> interface or send it to gmx-users-requ...@gromacs.org. >>> * Can't post? Read >>> http://www.gromacs.org/****Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists> >>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> > >>> >>> >> >> >> -- >> David A. Sáez San Martín >> Químico-Farmacéutico >> Concepción, Chile >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> * Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >> posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use thewww > interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- David A. Sáez San Martín Químico-Farmacéutico Concepción, Chile -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists