[gmx-users] strange continued jobs

[Albert]

HI Justin:

   thanks for such kind comments. I restart the job and it works fine now.

best
Albert



On 09/11/2012 12:50 PM, Justin Lemkul wrote:
>
>
> 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
>