From: Norman Geist (
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 []
Gesendet: Mittwoch, 27. Juli 2016 19:52
An: Norman Geist <>
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,



On Wed, Jul 27, 2016 at 1:04 AM, Norman Geist < <> > 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: <> [ <> ] Im Auftrag von Aliasghar Alizadeh-Mojarad
Gesendet: Mittwoch, 27. Juli 2016 05:05
An: Vmd l < <> >
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:



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.


Aliasghar Alizadeh-Mojarad
Aliasghar Alizadeh-Mojarad