[gmx-users] g_density problem

[郑仁慧]

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)