"onlyframes" is a 'trajout'-specific keyword. The script you gave
should kick back an error.
It would be nice to have "onlyframes" for trajin. Been on my to-do
list for probably years.
-Dan
On Thu, Mar 12, 2020 at 1:49 PM koushik kasavajhala
<koushik.sbiiit.gmail.com> wrote:
>
> Hi Dan,
>
> Why not use "onlyframes" keyword when writing particular frames instead of
> using first and last? Wouldn't the script below do the same as the one you
> suggested?
>
> parm myparm.parm7
> trajin mytraj.nc onlyframes 3000
> trajout frame3000.mol2
> run
>
> On Thu, Mar 12, 2020 at 1:46 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> > Hi,
> >
> > As others have alluded to, you can extract frames from trajectories
> > with cpptraj. If you want a frame at a specific time point, you can
> > calculate which one you need yourself - you just need to know what
> > time step you used (dt in Amber input) and the trajectory write
> > frequency in steps (ntwx in Amber input). For example, if you use a
> > time step of 1 fs (dt=0.001) and a write frequency of 1000 steps (i.e.
> > 1 frame per ps), then the frames in your trajectory will correspond to
> > 1 ps, 2 ps, 3 ps etc. In general, the time t (in ps) of each frame i
> > will be t = i * ntwx * dt (also, add an offset of initial time if
> > you're restarting a trajectory). Using that equation (assuming I
> > haven't made a mistake) you can relate any frame to any simulation
> > time. If you're using the netcdf trajectory format (which you should
> > be) you can actually check the time values in the file (via e.g.
> > ncdump -v time <file>).
> >
> > To extract say frame 3000 from your trajectory with cpptraj:
> >
> > parm myparm.parm7
> > trajin mytraj.nc 3000 3000
> > trajout frame3000.mol2
> > run
> >
> > Hope this helps,
> >
> > -Dan
> >
> >
> >
> > On Thu, Mar 12, 2020 at 3:42 AM Sruthi Sudhakar
> > <sruthisudhakarraji.gmail.com> wrote:
> > >
> > > Dear all,
> > > I have run a 500 ns production stage on a complex. ntwx = 1000 in the
> > input
> > > file. How can I extract a frame at, say for eg at 100 ns of the
> > production
> > > stage. There are a total of 250000 frames. Sorry if the question seems
> > too
> > > trivial.
> > > Thanking you in advance.
> > > Sruthi
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> >
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> >
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Received on Thu Mar 12 2020 - 11:00:03 PDT
