[gmx-users] Can not determine precision of trn file

[Yi Peng]

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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