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