VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Sep 19 2010 - 19:39:16 CDT
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- In reply to: Murpholino Peligro: "bigdcd + salt-bridge analysis"
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Hi,
You could either load a subset of frames from your trajectory
(e.g. skipping every 10 frames), or you could change the distance.tcl
and/or scripts you want to run to compute things within the bigdcd
style of script framework, incrementally.
Cheers,
John Stone
vmd_at_ks.uiuc.edu
On Thu, Sep 16, 2010 at 03:31:58PM -0500, Murpholino Peligro wrote:
> Is there any way to make the salt-bridge analysis frame by frame with bigdcd?
> I was experimenting with a petite trajectory and
> measure contacts
> and measure bond
> but i want selections per residues...not atoms
> like
> atomselect macro acidic "resname ASP GLU"
> atomselect macro acidic "resname ARG HIS LYS HSP"
> .
> .
> I try to do something like the distance.tcl.. from
> http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node7.html
> but....the problem is that the trajectory size is ~9 Gb..
>
> thanks :)
>
>
> --
> Mr. Murpholino X
>
> "mi segundo nombre es Peligro!!"
-- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns_at_ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
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