[gmx-users] Fatal error
Tsjerk Wassenaar
tsjerkw at gmail.com
Wed Jul 8 08:21:04 CEST 2009
Hi,
Probably you don't have write permissions in that folder.
Cheers,
Tsjerk
On Wed, Jul 8, 2009 at 1:07 AM, s lal badshah<shahbiochemist at yahoo.com> wrote:
> 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
> 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
> -[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
> frames
> -[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
> functions
> -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
>
> Total-Energy
>
> -------------------------------------------------------
> Program g_energy, VERSION 3.3.1
> Source code file: futil.c, line: 308
>
> File input/output error:
> md283-TE.xvg
> -------------------------------------------------------
>
> "No One Could Foresee the End That Came So Fast" (Slayer)
>
> syed at linux-g1cj:~/Desktop/283>
>
> Regards,
> LAL BADSHAH
>
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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