Hi,
On Thu, 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.
Did the script I posted earlier not work for you?
-Dan
>
> 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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>> >>>>>>
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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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--
-------------------------
Daniel R. Roe
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National Institutes of Health, NHLBI
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Received on Thu Jan 26 2017 - 08:30:02 PST
