From: Abhishek TYAGI (atyagiaa_at_connect.ust.hk)
Date: Wed Mar 18 2015 - 06:23:58 CDT
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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