[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  (-:
                              :-)  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)