[gmx-users] Disappear my solution

Morteza Khabiri khabiri at greentech.cz
Thu Aug 28 23:57:39 CEST 2008

Dear Justin

Thanks for your prompt reply and guide.

As you said I checked my files with gmxcheck.

My tpr file is ok. It includes water, hexan and protein. but my edr, xtc
and trr files have problem.
Their faults are as follow:

1- for xtc: Reading frame     110 time  550.000   Fatal error: Magic
Number Error in XTC file (read 0, should be 1995)

2- trr file: is empty

3- edr file: WARNING: there may be something wrong with energy file
Found: step=0, nre=0, ndisre=0, nblock=0, time=0.
Trying to skip frame expect a crash though

But when I look at my log file everything is ok. the last part of my log
file is:

           Step           Time         Lambda
        1357000     1357.00012        0.00000

   Energies (kJ/mol)
           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
    3.59479e+03    5.89878e+03    2.20709e+03    1.75877e+03    2.31501e+03
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)      Potential
    2.98386e+04    4.00479e+04   -4.96711e+03   -5.44333e+05   -4.63640e+05
    Kinetic En.   Total Energy    Temperature Pressure (bar)
    9.48193e+04   -3.68820e+05    3.02115e+02    4.16068e+01

I really confused and I dont know what is the problem or on the other hand
where is the problem. Because everything is ok till 1.3 ns after that the
problem appear. If there is some problem it should come at the first. why
it appear after this long time?

I attached my mdp file also.

Thanks for your attention and guidance.

Your sincerely,


Ph.D student of Biophysics
Laboratory of High performance computing
Institute of Systems Biology and Ecology ASCR
Institute of Physical Biology,
University of South Bohemia
Zamek 136 373 33, Nove Hrady
Czech Republic
Email: Khabiri at greentech.cz
mobile: +420 773 903 109
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