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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