AMBER Archive (2003)

Subject: Re: unifying trajectory files

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Wed Jun 25 2003 - 14:58:39 CDT

Hi,

Just a small suggestion, before unifying the trajectories it is good to
take a look at them (vizualize them) to see if there are any "wrong" frames.
If there are take those frames away from your unified trajectory.

e.g.
trajin name.mdcrd 1 500 1
trajin name1.mdcrd 510 1000 1
trajout unified.mdcrd

Ioana
On Wed, 25 Jun 2003, Natasja Brooijmans wrote:

> You can use ptraj
>
> Natasja Brooijmans, Ph.D.
> Visiting Post-Doctoral Scholar
> Kuntz Laboratory
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> San Francisco, CA 94143-2240
> phone: 415-476 3986
> fax: 415-502 1411
> e-mail: nbrooij_at_itsa.ucsf.edu
>
> On Wed, 25 Jun 2003, Peter Anderson wrote:
>
> > Dear Amber Users,
> >
> > I recently ran a 1-ns molecular dynamics simulation
> > that crashed a few times throughout the run. I thus
> > have several separate .mdcrd and .restrt files. Can
> > anyone tell me how I can combine the several
> > trajectory files together to get one integrated
> > trajectory file, if possible?
> >
> > Thank you very much,
> > Peter Anderson
> >
> > __________________________________
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>
>