thank you so much.
On Thu, Mar 12, 2020 at 2:36 PM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
> how many frames do you have in total? How many nanoseconds would that
> produce using your defined timestep? Number of nanoseconds / number of
> frames gives you time/frame. With this you should be able to calculate
> which frame you are looking for.
>
> // Gustaf
>
>
> > On 12 Mar 2020, at 09:12, Sruthi Sudhakar <sruthisudhakarraji.gmail.com>
> wrote:
> >
> > Sir,
> > I actually have difficulty in finding out the frame number corresponding
> to
> > a particular nanosecond.
> >
> > On Thu, Mar 12, 2020 at 1:30 PM Gustaf Olsson <gustaf.olsson.lnu.se>
> wrote:
> >
> >> I think ptraj can fix this for you, probably a lot of other tools as
> well,
> >> including VMD and Chimera with GUIs.
> >>
> >> for ptraj I think making an input file similar to this.
> >>
> >> parm [prmtop-file]
> >> trajin [mdcrd-file] first last step
> >> trajout [output file rst | ncrst | pdb | … ]
> >>
> >> Should get the job done. Just replace the “first” with the frame you
> want,
> >> “last” with the same frame and I suppose you can skip “step” or set it
> to
> >> 1, which I suspect is the default. There is probably easier ways to do
> this
> >> as well though this was the first that came to mind using the tools
> >> included in amber.
> >>
> >> // Gustaf
> >>
> >>
> >>> On 12 Mar 2020, at 08:41, 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 - 04:00:02 PDT
