Dear all:
For my trr file is large (2T), I use g_density to calculate the density of protein with a pbs file. However, when I qsub the pbs file, I cannot select the Group and there is fatal error. Can anybody solve the problem? Thank you very much for your help in advance. Sincerely Ren-hui Zhneg The following is the content of pbs file: #PBS -l nodes=node-0-16:ppn=16,walltime=40000:00:00 #PBS -N lka14 ##PBS -m abe #PBS -q default ##PBS -q q5620 ##################################### export PATH=/share/apps/gromacs/4.6.5/bin:$PATH WORKDIR=/home/zrh/md/lka14 ##################################### cd $WORKDIR g_density -f traj-lka14-216-cl-nvt10ns-step2fs-save10fs.trr -s lka14-216-cl-nvt10ns-save10fs.tpr -d z -o density-2z-10ns-10fs.xvg The following is the content of error file: :-) G R O M A C S (-: S C A M O R G :-) VERSION 4.6.5 (-: 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. :-) g_density (-: Option Filename Type Description ------------------------------------------------------------ -f traj-lka14-216-cl-nvt10ns-step2fs-save10fs.trr Input Trajectory: xtc trr trj gro g96 pdb cpt -n index.ndx Input, Opt. Index file -s lka14-216-cl-nvt10ns-save10fs.tpr Input Run input file: tpr tpb tpa -ei electrons.dat Input, Opt. Generic data file -o density-2z-10ns-10fs.xvg Output xvgr/xmgr 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 19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -[no]w bool no View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -d string z Take the normal on the membrane in direction X, Y or Z. -sl int 50 Divide the box in this number of slices. -dens enum mass Density: mass, number, charge or electron -ng int 1 Number of groups of which to compute densities. -[no]symm bool no Symmetrize the density along the axis, with respect to the center. Useful for bilayers. -[no]center bool no Shift the center of mass along the axis to zero. This means if your axis is Z and your box is bX, bY, bZ, the center of mass will be at bX/2, bY/2, 0. Reading file lka14-216-cl-nvt10ns-save10fs.tpr, VERSION 4.6.5 (single precision) Group 0 ( System) has 178104 elements Group 1 ( Protein) has 61992 elements Group 2 ( Protein-H) has 25704 elements Group 3 ( C-alpha) has 3024 elements Group 4 ( Backbone) has 9072 elements Group 5 ( MainChain) has 12312 elements Group 6 ( MainChain+Cb) has 15336 elements Group 7 ( MainChain+H) has 15768 elements Group 8 ( SideChain) has 46224 elements Group 9 ( SideChain-H) has 13392 elements Group 10 ( Prot-Masses) has 61992 elements Group 11 ( non-Protein) has 116112 elements Group 12 ( Water) has 114816 elements Group 13 ( SOL) has 114816 elements Group 14 ( non-Water) has 63288 elements Group 15 ( Ion) has 1296 elements Group 16 ( CL) has 1296 elements Group 17 ( Water_and_ions) has 116112 elements Select a group: ------------------------------------------------------- Program g_density, VERSION 4.6.5 Source code file: /home/liuh/gromacs-4.6.5/src/gmxlib/index.c, line: 1192 Fatal error: Cannot read from input For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "Ramones For Ever" (P.J. Van Maaren) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.