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,
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.
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:
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>