VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Jan 10 2017 - 03:18:54 CST

This sound like something went wrong while transferring the file. You might want to use rsync and its delta algorithm to copy the file, since it will be able to continue the download if it gets interrupted.

 

Are you copying by ssh?

 

Norman Geist

 

Von: sunyeping [mailto:sunyeping_at_aliyun.com]
Gesendet: Dienstag, 10. Januar 2017 10:04
An: Norman Geist <norman.geist_at_uni-greifswald.de>
Cc: vmd-l <vmd-l_at_ks.uiuc.edu>
Betreff: Re: AW: vmd-l: why vmd cannot load the dcd trajectory?

 

Dear Prof. Geist,

 

Thank you for reply. I am not familiar with the big-endian dcd. It was created in tianhe-2 and I don't wether it is big-endian. I have obtained many smaller dcd files from this system but they can all be corrected loaded into VMD, and I haven't met this error before. Since this dcd file is big, I cannot download the whole file yet from the tianhe-2 system. The downloading process always went wrong and stopped. The error of VMD loading is for the part dcd files. Do you think flipdcd is suitable for my situation.

 

Best regards.

 

Yeping Sun

------------------------------------------------------------------

From:Norman Geist <norman.geist_at_uni-greifswald.de <mailto:norman.geist_at_uni-greifswald.de> >

Time:2017 Jan 10 (Tue) 16:43

To:孙业平 < <mailto:sunyeping_at_aliyun.com> sunyeping_at_aliyun.com>

Cc:vmd-l <vmd-l_at_ks.uiuc.edu <mailto:vmd-l_at_ks.uiuc.edu> >

Subject:AW: vmd-l: why vmd cannot load the dcd trajectory?

 

Could it be a big-endian dcd (bluegene), maybe see „flipdcd“ ?

 

Von: owner-vmd-l_at_ks.uiuc.edu <mailto:owner-vmd-l_at_ks.uiuc.edu> [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von sunyeping
Gesendet: Dienstag, 10. Januar 2017 08:06
An: vmd-l < <mailto:vmd-l_at_ks.uiuc.edu> vmd-l_at_ks.uiuc.edu>
Betreff: vmd-l: why vmd cannot load the dcd trajectory?

 

Dear all,

 

I finished a namd simulation and get a 14 G dcd trajectory. However, this trajectory cannot be loaded into vmd. The following are the error message:

 

 

It has spent a large amount of my computational resources and time to get this trajectory, so if it is really corrupted and cannot be used, it would be a disaster for me?

 

Is there anyone who can help?

 

Best regards.

 

Yeping Sun

 


image001.png