VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Jul 28 2016 - 02:42:45 CDT

I guess not.

 

With some TCL scripting you could write PDB files for each frames of both DCD file out of VMD, merge these PDBs and convert the PDBs to a DCD at the end.

 

Von: Aliasghar Alizadeh-Mojarad [mailto:ali.alizadehmoj_at_gmail.com]
Gesendet: Mittwoch, 27. Juli 2016 19:52
An: Norman Geist <norman.geist_at_uni-greifswald.de>
Betreff: Re: vmd-l: merging independent dcd files,

 

Dear Norman,

Thank you for your reply. I resolved that problem. But, my problem is another thing. I want to merge two different dcd files with two different number of dummy atoms. I made an index file including total number of dummy atoms.

Does anybody know the developer of catdcd plugin? I even do not know it is possible to merge dcd files with different species and different number of particles or not.

 

Best wishes,

Ali

 

On Wed, Jul 27, 2016 at 1:04 AM, Norman Geist <norman.geist_at_uni-greifswald.de <mailto:norman.geist_at_uni-greifswald.de> > wrote:

If you run catdcd without argument it will print its usage information. It might be a good practice for you to figure this out by yourself, but:

 

catdcd –o merged.dcd –otype dcd –dcd file1.dcd –dcd file2.dcd

 

I think even shorter is possible with just:

 

catdcd –o merged.dcd file1.dcd file2.dcd

 

Von: owner-vmd-l_at_ks.uiuc.edu <mailto: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 Aliasghar Alizadeh-Mojarad
Gesendet: Mittwoch, 27. Juli 2016 05:05
An: Vmd l <vmd-l_at_ks.uiuc.edu <mailto:vmd-l_at_ks.uiuc.edu> >
Betreff: vmd-l: merging independent dcd files,

 

 

Dear VMD users,

I have two independent dcd files containing dummy atoms and I want to merge them. In fact, they are parts of the same trajectory file. I extracted them to do some processing(translating species to new coordination). Now, I want to combine them into a new trajectory.

I used catdcd plugin(I already searched in vmd mailing list) but I have problem with running catdcd. I got this error:

 

>>catdcd

wrong # args: should be "catdcdList dcdFileNames outFile indexFile stride"

 

It means that I have no catdcd pluging? I downloaded the binary catdcd but I do not know how I can use binaries to add as vmd plugin.

Is there another way to do it without using catdcd?

I will appreciate any helps.

  

-- 
Sincerely,
Aliasghar Alizadeh-Mojarad
  <http://thinkbeforeprinting.org/struct/signature-1.gif> 
 
-- 
Sincerely,
Aliasghar Alizadeh-Mojarad
  <http://thinkbeforeprinting.org/struct/signature-1.gif>