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
-------------------------------------------------------
"Don't Push Me, Cause I'm Close to the Edge" (Grandmaster Flash)
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