AMBER Archive (2006)

Subject: Re: AMBER: mdcrd file

From: Joseph Nachman (nachman_at_hera.med.utoronto.ca)
Date: Fri Sep 08 2006 - 12:36:42 CDT

You are right, and I'm still trying to figure out how to get
frames 1, 1000, 2000, 3000, 4000, 5000.

Joseph

On Thu, 7 Sep 2006, Brent Krueger wrote:

> Someone correct me if this is wrong, but I believe with the given
> ptraj script:
>
> >
> > trajin 5000_steps.binpos 1 5000 1000
> > trajout only_every_1000.binpos
> > go
>
>
> One would actually get frames 1000, 2000, 3000, 4000, and 5000.
>
>
> Cheers,
> Brent
>
>
>
> On Sep 7, 2006, at 1:39 PM, Mark Williamson wrote:
>
> > Jianhui wrote:
> >> Hello amber-users,
> >>
> >> I have run a system for 2ns and wrote down the mdcrd file every
> >> 1ps, which makes the mdcrd file too big to load completely in vmd.
> >> What I want to do is to select one frame every 2ps or 3ps second,
> >> is there any command in AMBER to do it? Thanks.
> >>
> >> Best regards,
> >>
> >> Jianhui
> >> tianj_at_rpi.edu
> >> 2006-09-07
> >>
> >>
> >> ---------------------------------------------------------------------
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> >
> > Dear Jianhui,
> >
> > (From the ptraj manual http://www.chpc.utah.edu/~cheatham/ptraj.html)
> >
> > One can specify a third parameter to ptraj's trajin command which is a
> > step offset. Hence with a trajectory file of 5000 steps, to extract
> > every 1000'th step to a new trajectory file one would use the
> > following
> > ptraj script:
> >
> >
> > trajin 5000_steps.binpos 1 5000 1000
> > trajout only_every_1000.binpos
> > go
> >
> > The distilled trajectory file "only_every_1000.binpos" would now
> > contain
> > only 5 steps from steps 1,1000,2000,3000 and 4000.
> >
> > regards,
> >
> > Mark
> >
> >
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>
> __________________________________________________________________
> Brent P. Krueger phone: 616 395 7629
> Assistant Professor fax: 616 395 7118
> Hope College SC 2120
> Department of Chemistry
> Holland, MI 49423
>
>
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> 

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