RE: Trajectory file formats & structural alignment

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed May 14 2008 - 00:15:17 CDT

Look up the "animate" command in the vmd manual. It will be something like
"animate write dcd [various arguments]".

-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of Wei Huang
Sent: Tuesday, May 13, 2008 9:57 PM
To: Giovanni Bellesia
Cc: namd_mailinglist
Subject: Re: namd-l: Trajectory file formats & structural alignment

Hi Giovanni,

Thanks! Actually I am using those two tools. I didn't realize that
catdcd can do that. I should have read the document carefully.

But to the second question. My problem is how can I output the result
after alignment into a new dcd file? I didn't find out rmsdtt can do
that.

Cheers,
Wei
On Thu, 2008-05-08 at 16:00 -0700, Giovanni Bellesia wrote:
> Hi,
>
> 1) catdcd 4.0
> http://www.ks.uiuc.edu/Development/MDTools/catdcd/
>
> 2) RMSD Trajectory Tool within VMD
> http://www.ks.uiuc.edu/Research/vmd/plugins/rmsdtt/
>
> BTW, both VMD and NAMD web pages contain a lot of information plus an
> extended set of links
> to documentation files and tutorials. Taking some time to go through
> them can be quite helpful !
>
> Giovanni
> > Dear VMD users,
> >
> > I have two question about manipulating trajectory file:
> >
> > 1) Is there any tool that can be used to convert DCD file to AMBER or
> > Gromacs trajectory file format?
> >
> > 2) How can I align the solute of my system in all my snapshots to that
> > of the first frame, and then output them into a new dcd file?
> >
> > Best,
> > Wei
> >
>
>

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