<DIV style="font-family:Arial,sans-serif;"><DIV><FONT face="Arial, sans-serif">Hello gromacs users,</FONT></DIV>
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<DIV><FONT face="Arial, sans-serif"> I ecountered the following error while performing the analysis of the MD run using the tpr and trr files.</FONT></DIV>
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<DIV><FONT face="Arial, sans-serif">Select a group: 1<BR>Selected 1: 'Protein'<BR>trn version: GMX_trn_file (single precision)<BR></FONT><FONT face="Arial, sans-serif">Reading frame 830 time 830.000 Fatal error: Can not determine precision of trn file, quit!<BR></FONT></DIV>
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<DIV><FONT face="Arial, sans-serif"> 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.</FONT></DIV>
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<DIV><FONT face="Arial, sans-serif"> Step Time Lambda<BR> 414750 829.50006 0.00000</FONT></DIV>
<DIV><FONT face="Arial, sans-serif"> Rel. Constraint Deviation: Max between atoms RMS<BR> Before LINCS 0.069666 2352 2353 0.006386<BR> After LINCS 0.000082 97 100 0.000022</FONT></DIV>
<DIV><FONT face="Arial, sans-serif"> Energies (kJ/mol)<BR> Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14<BR> 5.93016e+03 2.17805e+03 2.04973e+03 3.94265e+03 4.00753e+04<BR> LJ (SR) Coulomb (SR) Coulomb (LR) Potential Kinetic En.<BR> 5.81211e+04 -4.95081e+05 -1.22241e+05 -5.05025e+05 9.15110e+04<BR> Total Energy Temperature Pressure (bar)<BR> -4.13514e+05 3.00995e+02 5.71544e+01</FONT></DIV>
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<DIV><FONT face="Arial, sans-serif"> Step Time Lambda<BR> 415000 830.00006 0.00000</FONT></DIV>
<DIV><FONT face="Arial, sans-serif"> Rel. Constraint Deviation: Max between atoms RMS<BR> Before LINCS 0.055821 592 593 0.006322<BR> After LINCS 0.000092 737 740 0.000023</FONT></DIV>
<DIV><FONT face="Arial, sans-serif"> Energies (kJ/mol)<BR> Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14<BR> 5.92525e+03 2.23574e+03 2.12064e+03 3.87417e+03 4.00050e+04<BR> LJ (SR) Coulomb (SR) Coulomb (LR) Potential Kinetic En.<BR> 5.91018e+04 -4.95440e+05 -1.22146e+05 -5.04324e+05 9.08269e+04<BR> Total Energy Temperature Pressure (bar)<BR> -4.13497e+05 2.98745e+02 1.00768e+02</FONT></DIV>
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<DIV><FONT face="Arial, sans-serif"> Step Time Lambda<BR> 415250 830.50006 0.00000</FONT></DIV>
<DIV><FONT face="Arial, sans-serif"> Rel. Constraint Deviation: Max between atoms RMS<BR> Before LINCS 0.055036 2376 2377 0.006529<BR> After LINCS 0.000085 352 355 0.000023</FONT></DIV>
<DIV><FONT face="Arial, sans-serif"> Energies (kJ/mol)<BR> Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14<BR> 5.97620e+03 2.06364e+03 2.02333e+03 3.87432e+03 4.00435e+04<BR> LJ (SR) Coulomb (SR) Coulomb (LR) Potential Kinetic En.<BR> 5.84707e+04 -4.95169e+05 -1.22238e+05 -5.04956e+05 9.11952e+04<BR> Total Energy Temperature Pressure (bar)<BR> -4.13760e+05 2.99956e+02 6.63849e+01</FONT></DIV>
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<DIV><FONT face="Arial, sans-serif"> Step Time Lambda<BR> 415500 831.00006 0.00000</FONT></DIV>
<DIV><FONT face="Arial, sans-serif"> Rel. Constraint Deviation: Max between atoms RMS<BR> Before LINCS 0.053770 796 797 0.006382<BR> After LINCS 0.000074 211 213 0.000023</FONT></DIV>
<DIV><FONT face="Arial, sans-serif"> Energies (kJ/mol)<BR> Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14<BR> 5.88532e+03 2.09403e+03 2.03899e+03 3.88290e+03 4.00235e+04<BR> LJ (SR) Coulomb (SR) Coulomb (LR) Potential Kinetic En.<BR> 5.78752e+04 -4.93795e+05 -1.22139e+05 -5.04134e+05 9.10775e+04<BR> Total Energy Temperature Pressure (bar)<BR> -4.13057e+05 2.99569e+02 -3.85286e+01</FONT></DIV>
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<DIV><FONT face="Arial, sans-serif"> Step Time Lambda<BR> 500000 1000.00006 0.00000</FONT></DIV>
<DIV><FONT face="Arial, sans-serif"> Rel. Constraint Deviation: Max between atoms RMS<BR> Before LINCS 0.068457 1042 1043 0.006487<BR> After LINCS 0.000087 614 618 0.000022</FONT></DIV>
<DIV><FONT face="Arial, sans-serif"> Energies (kJ/mol)<BR> Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14<BR> 6.19012e+03 2.21099e+03 2.03782e+03 3.86956e+03 3.99484e+04<BR> LJ (SR) Coulomb (SR) Coulomb (LR) Potential Kinetic En.<BR> 5.86097e+04 -4.94645e+05 -1.22277e+05 -5.04055e+05 9.09963e+04<BR> Total Energy Temperature Pressure (bar)<BR> -4.13059e+05 2.99302e+02 1.08973e+02</FONT></DIV>
<DIV><BR><FONT face="Arial, sans-serif">Total NODE time on node 0: 886749<BR>Average NODE time: 443374<BR>Load imbalance reduced performance to 200% of max<BR></FONT></DIV>
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<DIV><FONT face="Arial, sans-serif"> 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.</FONT></DIV>
<DIV><BR><FONT face="Arial, sans-serif"> 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 :</FONT></DIV>
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<DIV><FONT face="Arial, sans-serif"> File Current start (ps) New start (ps)<BR>---------------------------------------------------------<BR> md.trr 0.000 ps 0<BR> mdnew.trr 800.000 ps 800</FONT></DIV>
<DIV><FONT face="Arial, sans-serif">Summary of files and start times used:</FONT></DIV>
<DIV><FONT face="Arial, sans-serif"> File Start time<BR>-----------------------------------------<BR> md.trr 0.000 ps<BR> mdnew.trr 800.000 ps</FONT></DIV>
<DIV><FONT face="Arial, sans-serif">Reading frame 0 time 0.000<BR>lasttime -12345<BR></FONT></DIV>
<DIV><FONT face="Arial, sans-serif">Continue writing frames from md.trr t=0 ps, frame=0</FONT></DIV>
<DIV><FONT face="Arial, sans-serif">Reading frame 830 time 830.000 Fatal error: Can not determine precision of trn file, quit!</FONT></DIV>
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<DIV><FONT face="Arial, sans-serif"><STRONG> </STRONG>Kindly let me know how to solve this problem. Anticipating a reply soon from the gromacs users.</FONT></DIV>
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<DIV><FONT face="Arial, sans-serif"> With regards,</FONT></DIV>
<DIV><FONT face="Arial, sans-serif"> prettina<BR>-------------------------------------------<BR><BR>Prettina Anto Louis<BR>Graduate Student<BR>Computational Biology & Bioinformatics Lab,<BR>Department of Biochemistry,<BR>National Core Research Center(NCRC)<BR>Gyeongsang National University<BR>900 Gazwa-dong, Jinju 660-701 Korea<BR>Email: prettina@bio.gnu.ac.kr<BR><BR>-------------------------------------------<BR><BR></FONT></DIV><BR> <BR><HR>I use Krify Mail - http://mail.krify.com Get yourmail at Krify today!</DIV>