Thanks Justin, I'm gonna take your advice. On Thu, Feb 14, 2013 at 11:43 AM, Justin Lemkul <jalem...@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> > > ==============================**========== > > -- > 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> > -- 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
