<div>Hi, everyone,</div>
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<div>I was using Gromacs-4.0.3 to run my MD calculations parallell on our High performance clusters for a large system which was crashed because I run out the time limits. So I tried to resume my calculations by the script as follows:</div>
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<div>mdrun -multi 16 -s md.tpr -f md.trr -e md.edr -o md.trr -g md.log -c md.gro -cpi state.cpt -append</div>
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<div>This worked well and give me the new .trr .edr .log files. </div>
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<div>But after I finished the resumed MD calculations, I tried to use g_rms or gmxcheck to analyze my trajectory .trr file and got the error.</div>
<div>gmxcheck -f md.trr</div>
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<div>The error is as follows:</div>
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<div>trn version: GMX_trn_file (single precision)<br>Reading frame 0 time 0.000<br># Atoms 426618<br>Reading frame 400 time 400.000<br>-------------------------------------------------------<br>Program gmxcheck, VERSION 4.0.3<br>
Source code file: trnio.c, line: 66</div>
<div>File input/output error:<br>Can not determine precision of trn file<br>-------------------------------------------------------</div>
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<div>I just wonder how can I solve this problem. I check the previous log file and found the previous crashed calculation</div>
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<div>"Received the TERM signal, stopping at the next step</div>
<div>241400 482.80002 0.00000</div>
<div> Energies (kJ/mol)<br> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14<br> 3.05829e+04 1.41875e+04 9.45860e+03 5.60788e+03 2.27543e+05<br> LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. Potential<br>
1.14629e+06 -1.99329e+04 -7.15141e+06 -8.30847e+05 -6.56851e+06<br> Kinetic En. Total Energy Temperature Pressure (bar) Cons. rmsd ()<br> 1.06339e+06 -5.50513e+06 2.99863e+02 1.54702e+01 2.08607e-05</div>
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<div>Received the TERM signal, stopping at the next step</div>
<div>241500 483.00003 0.00000"</div>
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<div>I checked the new log file and found the resumed calculations started from 241500. So what's wrong with the resumed calculations? </div>
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<div>I have read many discussions about the broken trr files. Most of people suggest to restart the calculations. But I am afraid of that I will get the same thing out if I use the same checkpoint file. I am looking forward to hearing from you.</div>
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<div>Sincerely,</div>
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<div>Yi Peng</div>
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