Hi, everyone, 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:
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 This worked well and give me the new .trr .edr .log files. 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. gmxcheck -f md.trr The error is as follows: trn version: GMX_trn_file (single precision) Reading frame 0 time 0.000 # Atoms 426618 Reading frame 400 time 400.000 ------------------------------------------------------- Program gmxcheck, VERSION 4.0.3 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file ------------------------------------------------------- I just wonder how can I solve this problem. I check the previous log file and found the previous crashed calculation "Received the TERM signal, stopping at the next step 241400 482.80002 0.00000 Energies (kJ/mol) G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 3.05829e+04 1.41875e+04 9.45860e+03 5.60788e+03 2.27543e+05 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. Potential 1.14629e+06 -1.99329e+04 -7.15141e+06 -8.30847e+05 -6.56851e+06 Kinetic En. Total Energy Temperature Pressure (bar) Cons. rmsd () 1.06339e+06 -5.50513e+06 2.99863e+02 1.54702e+01 2.08607e-05 Received the TERM signal, stopping at the next step 241500 483.00003 0.00000" I checked the new log file and found the resumed calculations started from 241500. So what's wrong with the resumed calculations? 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. Sincerely, Yi Peng
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