[gmx-users] Fatal error

s lal badshah shahbiochemist at yahoo.com
Wed Jul 8 01:07:16 CEST 2009

Hi Gromacs user,

I changed the version and this time it gave the following error
syed at linux-g1cj:~/Desktop/283> g_energy -f md283.edr -o md283-TE.xvg
                         :-)  G  R  O  M  A  C  S  (-:

                     Gnomes, ROck Monsters And Chili Sauce

                            :-)  VERSION 3.3.1  (-:

      Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
             Copyright (c) 2001-2006, 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.

                               :-)  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 xml
  -o   md283-TE.xvg  Output       xvgr/xmgr file
-viol  violaver.xvg  Output, Opt. xvgr/xmgr file
-pairs    pairs.xvg  Output, Opt. xvgr/xmgr file
-ora    orienta.xvg  Output, Opt. xvgr/xmgr file
-ort    orientt.xvg  Output, Opt. xvgr/xmgr file
-oda    orideva.xvg  Output, Opt. xvgr/xmgr file
-odr    oridevr.xvg  Output, Opt. xvgr/xmgr file
-odt    oridevt.xvg  Output, Opt. xvgr/xmgr file
-oten    oriten.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
       -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
      -[no]w   bool     no  View output xvg, xpm, eps and pdb files
   -[no]xvgr   bool    yes  Add specific codes (legends etc.) in the output
                            xvg files for the xmgrace program
    -[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
       -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
 -[no]orinst   bool     no  Analyse instantaneous orientation data
   -[no]ovec   bool     no  Also plot the eigenvectors with -oten
     -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, vac,
                            exp5, exp7 or exp9
     -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
Angle            Proper-Dih.      Ryckaert-Bell.   LJ-14            
Coulomb-14       LJ-(SR)          LJ-(LR)          Coulomb-(SR)     
Coul.-recip.     Position-Rest.   Potential        Kinetic-En.      
Total-Energy     Temperature      Pressure-(bar)   Box-X            
Box-Y            Box-Z            Volume           Density-(SI)     
pV               Vir-XX           Vir-XY           Vir-XZ           
Vir-YX           Vir-YY           Vir-YZ           Vir-ZX           
Vir-ZY           Vir-ZZ           Pres-XX-(bar)    Pres-XY-(bar)    
Pres-XZ-(bar)    Pres-YX-(bar)    Pres-YY-(bar)    Pres-YZ-(bar)    
Pres-ZX-(bar)    Pres-ZY-(bar)    Pres-ZZ-(bar)    #Surf*SurfTen    
Pcoupl-Mu-XX     Pcoupl-Mu-YY     Pcoupl-Mu-ZZ     Mu-X             
Mu-Y             Mu-Z             T-Protein        T-Non-Protein    
Lamb-Protein     Lamb-Non-Protein 


Program g_energy, VERSION 3.3.1
Source code file: futil.c, line: 308

File input/output error:

"No One Could Foresee the End That Came So Fast" (Slayer)

syed at linux-g1cj:~/Desktop/283> 


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