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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Received on Thu Mar 12 2020 - 11:00:01 PDT
