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
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>>>>
>>>>
>>>>
>>>> --
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>> imprisoned
>>>> here could not dream of heaven?
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Received on Thu Jan 26 2017 - 08:00:03 PST
