But why do you need to write each frame to nc format?
Hai
> On Jan 26, 2017, at 10:53 AM, Elisa Pieri <elisa.pieri90.gmail.com> wrote:
>
> No, sorry, I cannot use the PDB format, and I don't want to modify the
> frames by minimizing them. I just need them as they are in the nc format.
>
> Elisa
>
>> On Thu, Jan 26, 2017 at 4:47 PM, Adrian Roitberg <roitberg.ufl.edu> wrote:
>>
>> 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: giovedì 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 - 08:00:07 PST
