Re: DCD Error

From: manish kesherwani (manish221288_at_gmail.com)
Date: Wed Mar 18 2015 - 08:10:18 CDT

Hi , you download catdcd script from vmd script center then you run it. It
is working properly for combining in big trajactory.

On Wed, Mar 18, 2015 at 4:23 AM, Abhishek TYAGI <atyagiaa_at_connect.ust.hk>
wrote:

> 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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