[gmx-users] Fatal error: Can't determine precision of trn file, quit!

Prettina Anto_Louis Sun, 15 Oct 2006 19:46:02 -0700

Hello gromacs users,

I ecountered the following error while performing the analysis of the MD run using the tpr and trr files.

Select a group: 1
Selected 1: 'Protein'
trn version: GMX_trn_file (single precision)
Reading frame 830 time 830.000 Fatal error: Can not determine precision of trn file, quit!

The following is the md run log file extract , which shows that run there was no problem in the course of the md run:It was a 1ns md run.

Step Time Lambda
414750 829.50006 0.00000

   Rel. Constraint Deviation: Max    between atoms     RMS
       Before LINCS         0.069666   2352   2353   0.006386
        After LINCS         0.000082     97    100   0.000022

   Energies (kJ/mol)
          Angle    Proper Dih. Improper Dih.          LJ-14     Coulomb-14
    5.93016e+03    2.17805e+03    2.04973e+03    3.94265e+03    4.00753e+04
        LJ (SR)   Coulomb (SR)   Coulomb (LR)      Potential    Kinetic En.
    5.81211e+04   -4.95081e+05   -1.22241e+05   -5.05025e+05    9.15110e+04
   Total Energy    Temperature Pressure (bar)
   -4.13514e+05    3.00995e+02    5.71544e+01

Step Time Lambda
415000 830.00006 0.00000

   Rel. Constraint Deviation: Max    between atoms     RMS
       Before LINCS         0.055821    592    593   0.006322
        After LINCS         0.000092    737    740   0.000023

   Energies (kJ/mol)
          Angle    Proper Dih. Improper Dih.          LJ-14     Coulomb-14
    5.92525e+03    2.23574e+03    2.12064e+03    3.87417e+03    4.00050e+04
        LJ (SR)   Coulomb (SR)   Coulomb (LR)      Potential    Kinetic En.
    5.91018e+04   -4.95440e+05   -1.22146e+05   -5.04324e+05    9.08269e+04
   Total Energy    Temperature Pressure (bar)
   -4.13497e+05    2.98745e+02    1.00768e+02

Step Time Lambda
415250 830.50006 0.00000

   Rel. Constraint Deviation: Max    between atoms     RMS
       Before LINCS         0.055036   2376   2377   0.006529
        After LINCS         0.000085    352    355   0.000023

   Energies (kJ/mol)
          Angle    Proper Dih. Improper Dih.          LJ-14     Coulomb-14
    5.97620e+03    2.06364e+03    2.02333e+03    3.87432e+03    4.00435e+04
        LJ (SR)   Coulomb (SR)   Coulomb (LR)      Potential    Kinetic En.
    5.84707e+04   -4.95169e+05   -1.22238e+05   -5.04956e+05    9.11952e+04
   Total Energy    Temperature Pressure (bar)
   -4.13760e+05    2.99956e+02    6.63849e+01

Step Time Lambda
415500 831.00006 0.00000

   Rel. Constraint Deviation: Max    between atoms     RMS
       Before LINCS         0.053770    796    797   0.006382
        After LINCS         0.000074    211    213   0.000023

   Energies (kJ/mol)
          Angle    Proper Dih. Improper Dih.          LJ-14     Coulomb-14
    5.88532e+03    2.09403e+03    2.03899e+03    3.88290e+03    4.00235e+04
        LJ (SR)   Coulomb (SR)   Coulomb (LR)      Potential    Kinetic En.
    5.78752e+04   -4.93795e+05   -1.22139e+05   -5.04134e+05    9.10775e+04
   Total Energy    Temperature Pressure (bar)
   -4.13057e+05    2.99569e+02   -3.85286e+01

------

Step Time Lambda
500000 1000.00006 0.00000

   Rel. Constraint Deviation: Max    between atoms     RMS
       Before LINCS         0.068457   1042   1043   0.006487
        After LINCS         0.000087    614    618   0.000022

   Energies (kJ/mol)
          Angle    Proper Dih. Improper Dih.          LJ-14     Coulomb-14
    6.19012e+03    2.21099e+03    2.03782e+03    3.86956e+03    3.99484e+04
        LJ (SR)   Coulomb (SR)   Coulomb (LR)      Potential    Kinetic En.
    5.86097e+04   -4.94645e+05   -1.22277e+05   -5.04055e+05    9.09963e+04
   Total Energy    Temperature Pressure (bar)
   -4.13059e+05    2.99302e+02    1.08973e+02

Total NODE time on node 0: 886749
Average NODE time: 443374
Load imbalance reduced performance to 200% of max

----

---

Since there is a problem in the 830ps I am not able to use the trr file for my MD analysis part.I even tried to rerun the MD from few ps before the problematic ps, but while concatenating the trr files I faced the same problem at the 830 ps of the previous trr files.

Kindly please let me know, what is the real problem behind it, why it is showing such an error? What can be done to rectify the same. Also please do let me know how to assign the endtime while concatenating the 2 trr files. There is an option to mention the starting time for the respective trr files to be concatenated, but there is no option to mention the end time in the trjcat command for each trr files. If we don't specify the end time for the first trr file, then it stops with the same error :

File             Current start (ps) New start (ps)
---------------------------------------------------------
                   md.trr        0.000 ps          0
                mdnew.trr      800.000 ps          800

Summary of files and start times used:

          File                Start time
-----------------------------------------
                   md.trr        0.000 ps
                mdnew.trr      800.000 ps

Reading frame 0 time 0.000
lasttime -12345

Continue writing frames from md.trr t=0 ps, frame=0

Reading frame 830 time 830.000 Fatal error: Can not determine precision of trn file, quit!

Kindly let me know how to solve this problem. Anticipating a reply soon from the gromacs users.

With regards,

prettina

-------------------------------------------

Prettina Anto Louis

Graduate Student

Computational Biology & Bioinformatics Lab,
Department of Biochemistry,
National Core Research Center(NCRC)
Gyeongsang National University
900 Gazwa-dong, Jinju 660-701 Korea
Email: [EMAIL PROTECTED]

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[gmx-users] Fatal error: Can't determine precision of trn file, quit!

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