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.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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Received on Sun Sep 10 2006 - 06:07:15 PDT
