[gmx-users] analysis eror

s lal badshah shahbiochemist at yahoo.com
Wed Jul 8 00:05:33 CEST 2009

Hi gromacs users.

I need help with the old data generated by gromacs. It is about a year older.
I used the command and the output is:
syed at linux-g1cj:~/Desktop/283> g_energy -f md283.edr -o 283te.xvg
                         :-)  G  R  O  M  A  C  S  (-:

                   Good gRace! Old Maple Actually Chews Slate

                            :-)  VERSION 3.0.5  (-:

       Copyright (c) 1991-2001, University of Groningen, The Netherlands
         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.

                               :-)  g_energy  (-:

Option     Filename  Type          Description
  -f      md283.edr  Input         Generic energy: edr ene
 -f2       ener.edr  Input, Opt.   Generic energy: edr ene
  -s      topol.tpr  Input, Opt.   Generic run input: tpr tpb tpa
  -o      283te.xvg  Output        xvgr/xmgr file
-viol  violaver.xvg  Output, Opt.  xvgr/xmgr file
-pairs    pairs.xvg  Output, Opt.  xvgr/xmgr file
-corr   enecorr.xvg  Output, Opt.  xvgr/xmgr file
-vis      visco.xvg  Output, Opt.  xvgr/xmgr file
-ravg  runavgdf.xvg  Output, Opt.  xvgr/xmgr 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
          -b   time     -1  First frame (ps) to read from trajectory
          -e   time     -1  Last frame (ps) to read from trajectory
      -[no]w   bool     no  View output xvg, xpm, eps and pdb files
    -[no]fee   bool     no  Do a free energy estimate
     -fetemp   real    300  Reference temperature for free energy calculation
       -zero   real      0  Subtract a zero-point energy
    -[no]sum   bool     no  Sum the energy terms selected rather than display
                            them all
     -[no]dp   bool     no  Print energies in high precision
  -[no]mutot   bool     no  Compute the total dipole moment from the components
       -skip    int      0  Skip number of frames between data points
   -[no]aver   bool     no  Print also the X1,t and sigma1,t, only if only 1
                            energy is requested
       -nmol    int      1  Number of molecules in your sample: the energies
                            are divided by this number
        -ndf    int      3  Number of degrees of freedom per molecule.
                            Necessary for calculating the heat capacity
   -[no]fluc   bool     no  Calculate autocorrelation of energy fluctuations
                            rather than energy itself
     -acflen    int     -1  Length of the ACF, default is half the number of
-[no]normalize bool    yes  Normalize ACF
          -P   enum      0  Order of Legendre polynomial for ACF (0 indicates
                            none): 0, 1, 2 or 3
      -fitfn   enum   none  Fit function: none, exp, aexp, exp_exp or vac
     -ncskip    int      0  Skip N points in the output file of correlation
   -beginfit   real      0  Time where to begin the exponential fit of the
                            correlation function
     -endfit   real     -1  Time where to end the exponential fit of the
                            correlation function, -1 is till the end

Opened md283.edr as single precision energy file
Select the terms you want from the following list
End your selection with 0
   1=         Angle   2=   Proper Dih.   3=Ryckaert-Bell.   4=         LJ-14
   5=    Coulomb-14   6=       LJ (SR)   7=       LJ (LR)   8=  Coulomb (SR)
   9=  Coul. recip.  10=Position Rest.  11=     Potential  12=   Kinetic En.
  13=  Total Energy  14=   Temperature  15=Pressure (bar)  16=         Box-X
  17=         Box-Y  18=         Box-Z  19=        Volume  20=  Density (SI)
  21=            pV  22=        Vir-XX  23=        Vir-XY  24=        Vir-XZ
  25=        Vir-YX  26=        Vir-YY  27=        Vir-YZ  28=        Vir-ZX
  29=        Vir-ZY  30=        Vir-ZZ  31= Pres-XX (bar)  32= Pres-XY (bar)
  33= Pres-XZ (bar)  34= Pres-YX (bar)  35= Pres-YY (bar)  36= Pres-YZ (bar)
  37= Pres-ZX (bar)  38= Pres-ZY (bar)  39= Pres-ZZ (bar)  40= #Surf*SurfTen
  41=  Pcoupl-Mu-XX  42=  Pcoupl-Mu-YY  43=  Pcoupl-Mu-ZZ  44=          Mu-X
  45=          Mu-Y  46=          Mu-Z  47=     T-Protein  48= T-Non-Protein
  49=  Lamb-Protein  50=Lamb-Non-Protein
Fatal error: Could not open 283te.xvg
syed at linux-g1cj:~/Desktop/283> 

your help is necessary for my success.


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