AMBER Archive (2006)

Subject: Re: AMBER: mdcrd file

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Fri Sep 08 2006 - 15:54:34 CDT

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
>>>>
>>>>
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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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