Re: [AMBER] Split a trajectory into frames

From: Adrian Roitberg <roitberg.ufl.edu>
Date: Thu, 26 Jan 2017 10:47:47 -0500

If you want to use amber itself to then look at the individual frames,
let's say by minimizing them one by one, you can use the imin=5 option
is amber.

adrian


On 1/26/17 10:45 AM, Casalini Tommaso wrote:
> If pdb format is suitable as well for your purposes, you can use the keyword "multi" in the trajout command.
>
> Tommaso
> ________________________________________
> Da: Elisa Pieri [elisa.pieri90.gmail.com]
> Inviato: giovedý 26 gennaio 2017 16.42
> A: AMBER Mailing List
> Oggetto: Re: [AMBER] Split a trajectory into frames
>
> I need to get the individual frames in the nc format, like you would get
> using cpptraj with:
> trajin bigfile.nc 1 1 1
> trajout frame_00001.nc
>
> Elisa
>
> On Thu, Jan 26, 2017 at 4:38 PM, Nhai <nhai.qn.gmail.com> wrote:
>
>> Well, if we know clearly why do you need that, we might provide better
>> advice to optimize your workflow. (Or if we even have an existing tool for
>> your need).
>>
>> Hai
>>
>>> On Jan 26, 2017, at 10:30 AM, Elisa Pieri <elisa.pieri90.gmail.com>
>> wrote:
>>> Is this relevant ? :)
>>>
>>> I need to work on the frames individually.
>>>
>>> Elisa
>>>
>>>> On Thu, Jan 26, 2017 at 4:26 PM, Nhai <nhai.qn.gmail.com> wrote:
>>>>
>>>> The question is: why do you want yo do that?
>>>>
>>>> Hai
>>>>
>>>>> On Jan 26, 2017, at 10:10 AM, Elisa Pieri <elisa.pieri90.gmail.com>
>>>> wrote:
>>>>> Thanks Kenneth,
>>>>>
>>>>> yes that's my question too. Being a big file, it could take days to
>> load
>>>> it
>>>>> 40000 times! My other plan would be to split it in smaller files, and
>>>> then
>>>>> split them and so on..but this would be very annoying.
>>>>>
>>>>> Elisa
>>>>>
>>>>> On Thu, Jan 26, 2017 at 3:50 PM, Kenneth Huang <
>>>> kennethneltharion.gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> The best way I've found to split by every frame is to loop it through
>> a
>>>>>> shell script that ticks up after every frame, which at least automates
>>>> the
>>>>>> process and saves you from having to making a trajin for every 40000
>>>>>> frames, so something like-
>>>>>>
>>>>>> firstframe=1
>>>>>> lastframe=40000
>>>>>>
>>>>>> while [ $firstframe -le $lastframe ]; do
>>>>>>
>>>>>> cat >analysis.ptraj<<EOF
>>>>>> parm *.prmtop
>>>>>> trajin *.nc $firstframe $firstframe 1
>>>>>> trajout snapshot_$firstframe.pdb
>>>>>> EOF
>>>>>>
>>>>>> let firstframe=firstframe+1
>>>>>>
>>>>>> done
>>>>>>
>>>>>> I'd also be curious if there's a faster way that doesn't require
>>>> reloading
>>>>>> the trajectory every single time, though.
>>>>>>
>>>>>> Best,
>>>>>>
>>>>>> Kenneth
>>>>>>
>>>>>> On Thu, Jan 26, 2017 at 9:35 AM, Elisa Pieri <elisa.pieri90.gmail.com
>>>>>> wrote:
>>>>>>
>>>>>>> Hello,
>>>>>>>
>>>>>>> how can I split a .nc file into single frames? My nc file has 40000
>>>>>> frames
>>>>>>> and is 4.2 Gb, I think that using a strategy like "trajin mdcrd 1
>> 4000
>>>> 1
>>>>>> ;
>>>>>>> trajout mdcrd_chunk_" would be reeeeeally long. Anything faster?
>>>>>>>
>>>>>>> Thanks!
>>>>>>> Elisa
>>>>>>> _______________________________________________
>>>>>>> AMBER mailing list
>>>>>>> AMBER.ambermd.org
>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Ask yourselves, all of you, what power would hell have if those
>>>> imprisoned
>>>>>> here could not dream of heaven?
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-- 
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Thu Jan 26 2017 - 08:00:05 PST
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