Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. running on compute-1-6.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_mdB2.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 2 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.45# 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: 4821 4818 writing run input file... There were 3 warnings gcq#171: "I'm a Jerk" (F. Black) :-) G R O M A C S (-: Gromacs Runs On Most of All Computer Systems :-) 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 2 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 "Never Get a Chance to Kick Ass" (The Amps) Permission denied, please try again. Permission denied, please try again. Permission denied. p0_27021: p4_error: Child process exited while making connection to remote process on www.rocksclusters.org: 0 /opt/mpich/gnu/bin/mpirun: line 1: 27021 Broken pipe /usr/local/gromacs/i686-pc-linux-gnu/bin/mdrun_mpi "-s" "/home/ahl/PO/topol/PO45s_mdB2" "-o" "/home/ahl/PO/ut2/PO45s_mdB2" "-c" "/home/ahl/PO/ut2/PO45s_mdB2" "-g" "/home/ahl/PO/ut2/PO45s_mdB2" "-e" "/home/ahl/PO/ut2/PO45s_mdB2" "-np" "2" -p4pg /home/ahl/PO/PI26925 -p4wd /home/ahl/PO