From: btreece_at_andrew.cmu.edu
Date: Wed Mar 18 2015 - 10:05:58 CDT
Abhi,
What are the file sizes for each?
Bradley
> Dear Josh,
>
> the log file is as follows:
>
>
> TIMING: 99999000 CPU: 1.22372e+06, 0.024316/step Wall: 1.22372e+06,
> 0.024316/step, 0.00675445 hours remaining, 713.925781 MB of memory in use.
> ENERGY: 99999000 1559.9895 2857.4765 2476.5506
> 24.8891 -644729.0421 83417.3582 369.5601 0.0000
> 82181.4611 -471841.7569 299.0941 -554023.2180
> -471677.3357 300.1053 -20758.0248 94.6445
> 1367630.1184 10.8342 10.8706
>
> PRESSURE: 100000000 -21209.7 411.919 -465.102 280.973 -21472.1 16.9422
> -366.092 174.739 -20903.4
> GPRESSURE: 100000000 -169.389 407.024 -547.253 305.837 -307.554 -33.7555
> -401.648 127.4 -514.401
> PRESSAVG: 100000000 -10.4791 9.51392 -51.2958 84.5688 1.1351 55.0474
> -96.1522 -13.0117 -59.8567
> GPRESSAVG: 100000000 -10.6852 9.1878 -51.6702 84.2353 1.02011 54.9018
> -96.312 -12.7367 -59.6655
> TIMING: 100000000 CPU: 1.22375e+06, 0.0244166/step Wall: 1.22375e+06,
> 0.0244166/step, 0 hours remaining, 713.929688 MB of memory in use.
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY MISC
> KINETIC TOTAL TEMP POTENTIAL
> TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME
> PRESSAVG GPRESSAVG
>
> ENERGY: 100000000 1578.6460 2839.1712 2494.6513
> 28.1142 -644220.4090 82951.3469 391.2504 0.0000
> 82455.8013 -471481.4278 300.0925 -553937.2291
> -471313.5083 300.3080 -21195.0447 -330.4479
> 1367630.1184 -23.0669 -23.1102
>
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 100000000
> WRITING COORDINATES TO DCD FILE Production_100.dcd AT STEP 100000000
> WRITING COORDINATES TO RESTART FILE AT STEP 100000000
> FINISHED WRITING RESTART COORDINATES
> WRITING VELOCITIES TO RESTART FILE AT STEP 100000000
> FINISHED WRITING RESTART VELOCITIES
> WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 100000000
> CLOSING EXTENDED SYSTEM TRAJECTORY FILE
> WRITING COORDINATES TO OUTPUT FILE AT STEP 100000000
> CLOSING COORDINATE DCD FILE Production_100.dcd
> WRITING VELOCITIES TO OUTPUT FILE AT STEP 100000000
> ====================================================
>
> WallClock: 1223748.000000 CPUTime: 1223748.000000 Memory: 713.941406 MB
> Program finished.
>
>
>> On 18 Mar, 2015, at 10:36 pm, Josh Vermaas <vermaas2_at_illinois.edu>
>> wrote:
>>
>> Hi Abhi,
>>
>> Did you check if the NAMD job terminated normally? Oftentimes during an
>> abnormal termination (such as when you hit the wallclock limit), the dcd
>> generated is too short for what the header claims. Since the header is
>> written at the beginning of the simulation, the dcd header will claim a
>> framecount based on the number of steps you are planning to run. What
>> are the filesizes for the dcds in question? Is the sum of the sizes for
>> Production.dcd and Production_1.dcd equal to that of Production_100.dcd?
>> Catdcd is telling you no, so if I were to bet, I'd assume that the last
>> simulation terminated abnormally (check the logfile!).
>>
>> -Josh
>>
>> On 3/18/15 8:29 AM, Abhishek Tyagi wrote:
>>> Thankyou for your reply,
>>>
>>> I have again checked it, I am a bit confused, could you suggest what
>>> else could be done in this
>>>
>>> Thanks
>>>
>>> ABhi
>>>
>>>> On 18 Mar, 2015, at 10:27 pm, btreece_at_andrew.cmu.edu wrote:
>>>>
>>>> Hi Abhi,
>>>>
>>>> After reading your output, it appears there is an issue with
>>>> Production_100.dcd. The other two wrote 50001 frames and the header
>>>> for
>>>> Production_100.dcd claimed to have the other 50000, but only 23701
>>>> were
>>>> able to be read. I know you said you checked it, but I would inspect
>>>> that
>>>> file more closely. Perhaps you missed something?
>>>>
>>>> Bradley
>>>>
>>>>> Dear Experts,
>>>>>
>>>>> I am using NAMD 2.10 on gpu cluster, initially I had performed MD for
>>>>> 50ns, when I restarted from 50 to 100ns, the MD finishes
>>>>> successfully.
>>>>> Finally, I was trying to use catdcd to merge these files in to one
>>>>> big dcd
>>>>> file as follows:
>>>>> This is first time I am experiencing this error.
>>>>>
>>>>>
>>>>> catdcd -o full-100.dcd Production.dcd Prodution_1.dcd
>>>>> Production_100.dcd
>>>>> CatDCD 4.0
>>>>> dcdplugin) detected standard 32-bit DCD file of native endianness
>>>>> dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
>>>>> Opening file 'full-100.dcd' for writing.
>>>>> dcdplugin) detected standard 32-bit DCD file of native endianness
>>>>> dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
>>>>> Opened file 'Production.dcd' for reading.
>>>>> Read 13157 frames from file Production.dcd, wrote 13157.
>>>>> dcdplugin) detected standard 32-bit DCD file of native endianness
>>>>> dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
>>>>> Opened file 'Prodution_1.dcd' for reading.
>>>>> Read 36844 frames from file Prodution_1.dcd, wrote 36844.
>>>>> dcdplugin) detected standard 32-bit DCD file of native endianness
>>>>> dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
>>>>> dcdplugin) Warning: DCD header claims 50000 frames, file size
>>>>> indicates
>>>>> there are actually 23071 frames
>>>>> Opened file 'Production_100.dcd' for reading.
>>>>> Read 23071 frames from file Production_100.dcd, wrote 23071.
>>>>> Total frames: 73072
>>>>> Frames written: 73072
>>>>> CatDCD exited normally.
>>>>>
>>>>>
>>>>> ?What is doubtful here is the number of frames should be 100000 but
>>>>> these
>>>>> are 73000, I checked these trajectories in vmd and i cant see any
>>>>> problem
>>>>> their.
>>>>>
>>>>> Could you please tell me what is happened to this MD.
>>>>>
>>>>>
>>>>> Thanks in advance
>>>>>
>>>>>
>>>>> Abhi
>>>>>
>>>
>>
>
>
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