[gmx-users] strange continued jobs

[Albert]

hello:

   I've restart my jobs with command:

mpiexec -n 160 /opt/gromacs/4.5.5/bin/mdrun -nosum -dlb yes -v -s md.tpr 
-npme 20 -o md2.trr -g md2.log -e md2.edr -cpi

The previous log file is:


--------------------log---one---------------------------
DD  step 113469999  vol min/aver 0.540! load imb.: force 40.5%  pme 
mesh/force 0.629

            Step           Time         Lambda
       113470000   226940.00000        0.00000

    Energies (kJ/mol)
           Angle            U-B    Proper Dih.  Improper Dih. CMAP Dih.
     1.70355e+02    4.99014e+04    3.43419e+04    8.47175e+02 -1.29907e+03
           LJ-14     Coulomb-14        LJ (SR)        LJ (LR) Disper. corr.
     1.00912e+04   -5.66686e+03    1.58148e+04   -4.31489e+02 -4.61752e+03
    Coulomb (SR)   Coul. recip.      Potential    Kinetic En.   Total Energy
    -4.29387e+05   -9.64431e+04   -4.26678e+05    1.22078e+05 -3.04600e+05
     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
     3.03352e+02   -1.64273e+02    6.28299e+01    1.75083e-05
-------------------------------------------------------------


After I continued the job, I found my log file is the following:


------------------long----------two--------------------

DD  step 86759999  vol min/aver 0.450! load imb.: force 38.0%  pme 
mesh/force 0.771

            Step           Time         Lambda
        86760000   173520.00000        0.00000

    Energies (kJ/mol)
           Angle            U-B    Proper Dih.  Improper Dih. CMAP Dih.
     1.53725e+02    5.06175e+04    3.48843e+04    8.51459e+02 -1.35598e+03
           LJ-14     Coulomb-14        LJ (SR)        LJ (LR) Disper. corr.
     1.02049e+04   -6.48180e+03    1.63099e+04   -4.31662e+02 -4.62554e+03
    Coulomb (SR)   Coul. recip.      Potential    Kinetic En.   Total Energy
    -4.29154e+05   -9.60364e+04   -4.25064e+05    1.21298e+05 -3.03766e+05
     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
     3.01413e+02   -1.64844e+02   -7.07993e+01    1.74002e-05
-----------------------------------------------------


obviously, the continued job didn't wirte log based on previous time.

I am just wondering is it OK for this continued job when I am trying to 
merged it with previous after it is finished?

Also I found that the trjconv command doesn't work when I try to extract 
trajectory for analyis:



trjconv -f md2.trr -s md.tpr -pbc mol -o md2.xtc

-------------------------error-------------------------------------
Select a group: 0
Selected 0: 'System'
trn version: GMX_trn_file (single precision)
Reading frame       0 time 2000.000
Setting output precision to 0.001 (nm)

-------------------------------------------------------
Program trjconv, VERSION 4.5.5
Source code file: futil.c, line: 459

File input/output error:
md2.xtc
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

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