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?
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
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> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Jan 26 2017 - 08:00:04 PST
