From: Abhishek Tyagi (atyagiaa_at_connect.ust.hk)
Date: Wed Mar 18 2015 - 09:29:42 CDT
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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