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Hi,<BR> <BR>I am new for gromacs, I am trying to run the mdrun-gpu executable:<BR> <BR>the step to build the mdrun-gpu:<BR> <BR>1. disable the shared libraries:<BR> //disable shared libraries (can be problematic with MPI, Windows)<BR> BUILD_SHARED_LIBS:BOOL=OFF<BR>2. export LD_LIBRARY_PATH=/path to openmm2.0-Linux64/lib:$ LD_LIBRARY_PATH<BR>3. export OPENMM_PLUGIN_DIR=/path to openmm2.0-Linux64/plugins<BR>4. export OPENMM_ROOT_DIR=/path to openmm2.0-Linux64<BR>5. ./configure<BR>6. cmake -DGMX_OPENMM=ON<BR>7. make mdrun<BR>8. make install<BR> <BR>when I got the mdrun-gpu in /src/kernel. <BR> <BR>I put all the shared libs in one folder, point the LD_LIBRARY_PATH to this folder, also openmm libs<BR> <BR>The attached is the .tpr file I use in the same folder with mdrun-gpu.<BR> <BR>when i run ./mdrun-gpu<BR>it shows:<BR><BR> :-) G R O M A C S (-:<BR> GROningen MAchine for Chemical Simulation<BR> :-) VERSION 4.5.1 (-:<BR> Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,<BR> Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,<BR> Gerrit Groenhof, Peter Kasson, Per Larsson, Peiter Meulenhoff,<BR> Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schultz,<BR> Michael Shirts, Alfons Sijbers, Peter Tieleman,<BR> Berk Hess, David van der Spoel, and Erik Lindahl.<BR> Copyright (c) 1991-2000, University of Groningen, The Netherlands.<BR> Copyright (c) 2001-2010, The GROMACS development team at<BR> Uppsala University & The Royal Institute of Technology, Sweden.<BR> check out <A href="http://www.gromacs.org/" target=_blank><FONT color=#0068cf>http://www.gromacs.org</FONT></A> for more information.<BR> This program is free software; you can redistribute it and/or<BR> modify it under the terms of the GNU General Public License<BR> as published by the Free Software Foundation; either version 2<BR> of the License, or (at your option) any later version.<BR> :-) ./mdrun-gpu (-:<BR>Option Filename Type Description<BR>------------------------------------------------------------<BR> -s topol.tpr Input Run input file: tpr tpb tpa<BR> -o traj.trr Output Full precision trajectory: trr trj cpt<BR> -x traj.xtc Output, Opt. Compressed trajectory (portable xdr format)<BR>-cpi state.cpt Input, Opt. Checkpoint file<BR>-cpo state.cpt Output, Opt. Checkpoint file<BR> -c confout.gro Output Structure file: gro g96 pdb etc.<BR> -e ener.edr Output Energy file<BR> -g md.log Output Log file<BR>-dhdl dhdl.xvg Output, Opt. xvgr/xmgr file<BR>-field field.xvg Output, Opt. xvgr/xmgr file<BR>-table table.xvg Input, Opt. xvgr/xmgr file<BR>-tablep tablep.xvg Input, Opt. xvgr/xmgr file<BR>-tableb table.xvg Input, Opt. xvgr/xmgr file<BR>-rerun rerun.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt<BR>-tpi tpi.xvg Output, Opt. xvgr/xmgr file<BR>-tpid tpidist.xvg Output, Opt. xvgr/xmgr file<BR> -ei sam.edi Input, Opt. ED sampling input<BR> -eo sam.edo Output, Opt. ED sampling output<BR> -j wham.gct Input, Opt. General coupling stuff<BR> -jo bam.gct Output, Opt. General coupling stuff<BR>-ffout gct.xvg Output, Opt. xvgr/xmgr file<BR>-devout deviatie.xvg Output, Opt. xvgr/xmgr file<BR>-runav runaver.xvg Output, Opt. xvgr/xmgr file<BR> -px pullx.xvg Output, Opt. xvgr/xmgr file<BR> -pf pullf.xvg Output, Opt. xvgr/xmgr file<BR>-mtx nm.mtx Output, Opt. Hessian matrix<BR> -dn dipole.ndx Output, Opt. Index file<BR>Option Type Value Description<BR>------------------------------------------------------<BR>-[no]h bool no Print help info and quit<BR>-[no]version bool no Print version info and quit<BR>-nice int 0 Set the nicelevel<BR>-deffnm string Set the default filename for all file options<BR>-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none<BR>-[no]pd bool no Use particle decompostion<BR>-dd vector 0 0 0 Domain decomposition grid, 0 is optimize<BR>-npme int -1 Number of separate nodes to be used for PME, -1<BR> is guess<BR>-ddorder enum interleave DD node order: interleave, pp_pme or cartesian<BR>-[no]ddcheck bool yes Check for all bonded interactions with DD<BR>-rdd real 0 The maximum distance for bonded interactions with<BR> DD (nm), 0 is determine from initial coordinates<BR>-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate<BR>-dlb enum auto Dynamic load balancing (with DD): auto, no or yes<BR>-dds real 0.8 Minimum allowed dlb scaling of the DD cell size<BR>-gcom int -1 Global communication frequency<BR>-[no]v bool no Be loud and noisy<BR>-[no]compact bool yes Write a compact log file<BR>-[no]seppot bool no Write separate V and dVdl terms for each<BR> interaction type and node to the log file(s)<BR>-pforce real -1 Print all forces larger than this (kJ/mol nm)<BR>-[no]reprod bool no Try to avoid optimizations that affect binary<BR> reproducibility<BR>-cpt real 15 Checkpoint interval (minutes)<BR>-[no]cpnum bool no Keep and number checkpoint files<BR>-[no]append bool yes Append to previous output files when continuing<BR> from checkpoint instead of adding the simulation<BR> part number to all file names<BR>-maxh real -1 Terminate after 0.99 times this time (hours)<BR>-multi int 0 Do multiple simulations in parallel<BR>-replex int 0 Attempt replica exchange every # steps<BR>-reseed int -1 Seed for replica exchange, -1 is generate a seed<BR>-[no]ionize bool no Do a simulation including the effect of an X-Ray<BR> bombardment on your system<BR>-device string Device option string<BR><BR>Back Off! I just backed up md.log to ./#md.log.14#<BR>Reading file topol.tpr, VERSION 4.0.5 (single precision)<BR>Note: tpx file_version 58, software version 73<BR>Back Off! I just backed up ener.edr to ./#ener.edr.14#<BR>WARNING: OpenMM does not support leap-frog, will use velocity-verlet integrator.<BR><BR>-------------------------------------------------------<BR>Program mdrun-gpu, VERSION 4.5.1<BR><STRONG>Source code file: /root/BioWorkBench/TPPS/GROMACS/GROMACS-final/gromacs-4.5.1/src/kernel/openmm_wrapper.cpp, line: 555</STRONG><BR><STRONG>Fatal error:<BR>OpenMM supports only the following methods for electrostatics: NoCutoff (i.e. rcoulomb = rvdw = 0 ),Reaction-Field, Ewald or PME.<BR></STRONG>For more information and tips for troubleshooting, please check the GROMACS<BR>website at <A href="http://www.gromacs.org/Documentation/Errors" target=_blank><FONT color=#0068cf>http://www.gromacs.org/Documentation/Errors</FONT></A><BR>-------------------------------------------------------<BR>"Breaking the Law, Breaking the Law" (Judas Priest)<BR><BR> <BR>Could you please help take a look at it? Is there anything wrong with my input file? <BR> <BR>RHEL 5.4 gcc 4.1.2, CUDA 3.1<BR>yy<BR> </body>
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