AMBER Archive (2006)

Subject: Re: AMBER: mdcrd file

From: Mark Williamson (Mark.Williamson_at_imperial.ac.uk)
Date: Thu Sep 07 2006 - 12:39:12 CDT

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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