[gmx-users] installation
David Sáez
davidsaezsan at gmail.com
Thu Feb 14 15:40:23 CET 2013
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 <erikm at 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*
>> *$*
>>
>>
>> Nothing happened, the prompt returns normally and no action is executed.
>> Do
>> you have any idea?
>>
>>
>> On Tue, Feb 12, 2013 at 11:27 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 2/12/13 9:24 PM, David Sáez wrote:
>>>
>>> Hello everybody, I'm trying to install Gromacs 4.6 in my Ubuntu 12.04
>>>> laptop. As I am not a a skilled user, I tried the Quick and Dirty
>>>> Installation, After following the instructions I obtained this message
>>>> when
>>>> trying to execute GMXRC:
>>>>
>>>> david at HAL-9000:~$ /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>
>>> >
>>>
>>> ==============================****==========
>>>
>>> --
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>>> >
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>>>
>>>
>>
>>
>> --
>> David A. Sáez San Martín
>> Químico-Farmacéutico
>> Concepción, Chile
>> --
>> gmx-users mailing list gmx-users at gromacs.org
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>>
>
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--
David A. Sáez San Martín
Químico-Farmacéutico
Concepción, Chile
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