On 9/11/12 3:11 AM, Albert wrote:
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.
What's present in the .log file is rather irrelevant. What's important is the
contents of the .cpt file that was used as input for -cpi. Use gmxcheck to find
out what time from which the simulation should have continued. It seems odd
indeed that you would have gone back 50 ns, especially since the .cpt file
should be written every 15 minutes.
I am just wondering is it OK for this continued job when I am trying to merged
it with previous after it is finished?
Given the information at hand, there's nothing immediately "wrong" about what
you're seeing. Inconvenient, perhaps, to have lost time, but the contents of
the .cpt file used will confirm what should have happened.
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)
Do you have sufficient disk space? Read/write permissions?
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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