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?
> >>>>>> _______________________________________________
> >>>>>> 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
> >>>> _______________________________________________
> >>>> 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
> >> _______________________________________________
> >> 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
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Dr. Adrian E. Roitberg
> University of Florida Research Foundation Professor.
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
> _______________________________________________
> 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
Received on Thu Jan 26 2017 - 08:00:06 PST
