AMBER Archive (2006)

Subject: Re: AMBER: mdcrd file

From: Brent Krueger (kruegerb_at_hope.edu)
Date: Thu Sep 07 2006 - 21:55:27 CDT

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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