AMBER Archive (2006)

Subject: Re: AMBER: mdcrd file

From: Joseph Nachman (nachman_at_hera.med.utoronto.ca)
Date: Mon Sep 11 2006 - 13:00:21 CDT

Dear Dr. Simmerling -

Great idea - thanks!
Joseph

On Fri, 8 Sep 2006, Carlos Simmerling wrote:

> how about using two trajin lines and 1 trajout?
> the first trajin can be frame 1 only, and the next trajin can
> be 1000, 2000 etc.
>
> Joseph Nachman wrote:
> > 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
> >>>>
> >>>>
> >>>> ---------------------------------------------------------------------
> >>>> --
> >>>> The AMBER Mail Reflector
> >>>> To post, send mail to amber_at_scripps.edu
> >>>> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >>>>
> >>> 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
> >>>
> >>>
> >>> ----------------------------------------------------------------------
> >>> -
> >>> The AMBER Mail Reflector
> >>> To post, send mail to amber_at_scripps.edu
> >>> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >>>
> >> __________________________________________________________________
> >> 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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> >> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >>
> >>
> >
> >
>
>
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Joseph Nachman				Department of Biochemistry
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