Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. running on compute-1-5.local mkdir: cannot create directory `/home/ahl/PO/ut2': File exists creating /home/ahl/PO/ut2 Option Filename Type Description ------------------------------------------------------------ -f PO45s_mdX.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c PO45_Smith_1ns.gro Input Generic structure: gro g96 pdb tpr tpb tpa xml -r conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml -rb conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml -n PO45s.ndx Input, Opt! Index file -deshuf deshuf.ndx Output, Opt. Index file -p topol/21PO45s.top Input Topology file -pp processed.top Output, Opt. Topology file -o topol/PO45s_mdB7_2.tpr Output Generic run input: tpr tpb tpa xml -t traj.trr Input, Opt. Full precision trajectory: trr trj -e ener.edr Input, Opt. Generic energy: edr ene Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -nice int 0 Set the nicelevel -[no]v bool yes Be loud and noisy -time real -1 Take frame at or first after this time. -np int 7 Generate statusfile for # nodes -[no]shuffle bool no Shuffle molecules over nodes -[no]sort bool no Sort molecules according to X coordinate -[no]rmdumbds bool yes Remove constant bonded interactions with dummies -load string Releative load capacity of each node on a parallel machine. Be sure to use quotes around the string, which should contain a number for each node -maxwarn int 10 Number of warnings after which input processing stops -[no]check14 bool no Remove 1-4 interactions without Van der Waals -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Back Off! I just backed up mdout.mdp to ./#mdout.mdp.48# WARNING 1 [file PO45s_mdX.mdp, line unknown]: Unknown left-hand warnings in parameter file checking input for internal consistency... WARNING 2 [file PO45s_mdX.mdp, line unknown]: Removing the rotation around the center of mass in a periodic system (this is not a problem when you have only one molecule). Note: Old option for temperature coupling given: changing "yes" to "Berendsen" Generated 0 of the 21 non-bonded parameter combinations Excluding 3 bonded neighbours for PO45s 21 WARNING 3 [file "topol/21PO45s.top", line 16]: System has non-zero total charge: 2.464280e-05 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... initialising group options... processing index file... Not using any simulated annealing Making dummy/rest group for Acceleration containing 9639 elements Making dummy/rest group for Freeze containing 9639 elements Making dummy/rest group for VCM containing 9639 elements Number of degrees of freedom in T-Coupling group System is 28911.00 Making dummy/rest group for User1 containing 9639 elements Making dummy/rest group for User2 containing 9639 elements Making dummy/rest group for XTC containing 9639 elements Making dummy/rest group for Or. Res. Fit containing 9639 elements T-Coupling has 1 element(s): System Energy Mon. has 1 element(s): System Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1 has 1 element(s): rest User2 has 1 element(s): rest VCM has 1 element(s): rest XTC has 1 element(s): rest Or. Res. Fit has 1 element(s): rest Checking consistency between energy and charge groups... splitting topology... There are 2877 charge group borders and 9639 shake borders There are 2877 total borders Division over nodes in atoms: 1377 1377 1377 1377 1377 1377 1377 writing run input file... There were 3 warnings gcq#71: "I Want to Know Right Now" (Meatloaf) :-) G R O M A C S (-: GROup of MAchos and Cynical Suckers :-) VERSION 3.2.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2004, The GROMACS development team, 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 General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) /usr/local/gromacs/i686-pc-linux-gnu/bin/grompp_mpi (-: creating statusfile for 7 nodes... calling /usr/bin/cpp... processing topology... # BONDS: 28854 # ANGLES: 72912 # PDIHS: 151830 grompp done GMXBIN= /usr/local/gromacs/i686-pc-linux-gnu/bin /usr/local/gromacs/i686-pc-linux-gnu/bin/mdrun /usr/local/gromacs/i686-pc-linux-gnu/bin/mdrun_mpi "Uh-oh" (Tinky Winky) NNODES=7, MYRANK=0, HOSTNAME=compute-1-5.local NNODES=7, MYRANK=5, HOSTNAME=compute-1-0.local NNODES=7, MYRANK=2, HOSTNAME=compute-1-4.local NNODES=7, MYRANK=1, HOSTNAME=compute-1-4.local NNODES=7, MYRANK=6, HOSTNAME=compute-1-4.local NNODES=7, MYRANK=3, HOSTNAME=compute-1-2.local NNODES=7, MYRANK=4, HOSTNAME=compute-1-2.local NODEID=5 argc=13 NODEID=0 argc=13 NODEID=1 argc=13 NODEID=3 argc=13 NODEID=2 argc=13 NODEID=6 argc=13 NODEID=4 argc=13 :-) G R O M A C S (-: Gnomes, ROck Monsters And Chili Sauce :-) VERSION 3.2.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2004, The GROMACS development team, 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 General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) /usr/local/gromacs/i686-pc-linux-gnu/bin/mdrun_mpi (-: Option Filename Type Description ------------------------------------------------------------ -s /home/ahl/PO/topol/PO45s_mdB7_2.tpr Input Generic run input: tpr tpb tpa xml -o /home/ahl/PO/ut2/PO45s_mdB7_2.trr Output Full precision trajectory: trr trj -x traj.xtc Output, Opt. Compressed trajectory (portable xdr format) -c /home/ahl/PO/ut2/PO45s_mdB7_2.gro Output Generic structure: gro g96 pdb xml -e /home/ahl/PO/ut2/PO45s_mdB7_2.edr Output Generic energy: edr ene -g /home/ahl/PO/ut2/PO45s_mdB7_2.log Output Log file -dgdl dgdl.xvg Output, Opt. xvgr/xmgr file -field field.xvg Output, Opt. xvgr/xmgr file -table table.xvg Input, Opt. xvgr/xmgr file -rerun rerun.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb -ei sam.edi Input, Opt. ED sampling input -eo sam.edo Output, Opt. ED sampling output -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 -pi pull.ppa Input, Opt. Pull parameters -po pullout.ppa Output, Opt. Pull parameters -pd pull.pdo Output, Opt. Pull data output -pn pull.ndx Input, Opt. Index file -mtx nm.mtx Output, Opt. Hessian matrix -dn dipole.ndx Output, Opt. Index file Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -nice int 19 Set the nicelevel -deffnm string Set the default filename for all file options -np int 7 Number of nodes, must be the same as used for grompp -nt int 1 Number of threads to start on each node -[no]v bool no Be loud and noisy -[no]compact bool yes Write a compact log file -[no]multi bool no Do multiple simulations in parallel (only with -np > 1) -[no]glas bool no Do glass simulation with special long range corrections -[no]ionize bool no Do a simulation including the effect of an X-Ray bombardment on your system before, cr=5before, cr=0before, cr=3before, cr=1before, cr=4before, cr=2Reading file /home/ahl/PO/topol/PO45s_mdB7_2.tpr, VERSION 3.2.1 (single precision) before, cr=6starting mdrun '"21 PO_45 with Smith-potential"' 10 steps, 0.0 ps. Writing final coordinates. after, cr=4after, cr=5after, cr=1after, cr=6 M E G A - F L O P S A C C O U N T I N G Based on real time for parallel computer. RF=Reaction-field Free=Free Energy SC=Softcore T=Tabulated S=Solvent W=Water WW=Water-Water Computing: M-Number M-Flop's % Flop's Buckingham + Coul 79.503099 3180.123960 93.9 Innerloop-Iatom 0.383493 3.834930 0.1 NS-Pairs 3.774931 79.273551 2.3 Reset In Box 0.019278 0.173502 0.0 Shift-X 0.212058 1.272348 0.0 CG-CoM 0.005754 0.166866 0.0 Sum Forces 0.424116 0.424116 0.0 Bonds 0.105798 4.549314 0.1 Angles 0.200508 32.682804 1.0 Propers 0.334026 76.491954 2.3 Virial 0.108108 1.945944 0.1 Update 0.106029 3.286899 0.1 Stop-CM 0.096390 0.963900 0.0 Calc-Ekin 0.115668 3.123036 0.1 Total 3388.31312 100.0 NODE (s) Real (s) (%) Time: 7.000 7.000 100.0 (Mnbf/s) (MFlops) (ps/NODE hour) (NODE hour/ns) Performance: 11.358 484.045 1.286 777.778 after, cr=0after, cr=3after, cr=2p5_305: p4_error: Timeout in establishing connection to remote process: 0