• ## Outreach

From: Ashar Malik (asharjm_at_gmail.com)
Date: Thu Aug 17 2017 - 07:58:49 CDT

Seriously?
Do you know how to convert femto seconds to nano seconds?????

On Aug 18, 2017 12:27 AM, "Saikat Pal" <saikatpaliitg_at_yahoo.com> wrote:

> Thank you sir for your kind response.But I want to know how to convert
> frames to nano second in secondary structure analysis result.I have
> attached the file.
>
>
> Thank you
> Saikat
> On Wednesday 16 August 2017, 9:58:57 PM IST, Ashar Malik <
> asharjm_at_gmail.com> wrote:
>
>
> To the person who asked this:::
>
> Dear all,
> I have performed secondary structure analysis using VMD. I have get the
> result. I want to convert frames to nano seconds.What should I do ??
> Thanks and regards,
> Saikat
>
> You will need to look at the configuration file you used to run the
> simulation. If you used NAMD you will have to look for something like
>
> the time step you used, a common value is 2fs - yours may be different so
> look for it.
> the total number of steps you simulated for (N)
> the freq with which you saved frames to your trajectory (m)
>
> The way it works is that -
>
> if you run the simulation for N steps, with each step 2fs apart, you will
> basically have a total time of 2N femto seconds.
> but you were saving your frames to the trajectory every m-th step.
>
> if each step is 2fs then every consecutive frame would be 2m femto seconds
> apart.
>
> to double check this -- this relation should hold.
>
> Number of Frames (nF) = (N x 2fs) / m
>
> to convert between frames and time just solve
>
> 2fs x (frame number) x m
>
> the answer to the above will be time. This time value you will substitute
> for the frame number on the x-axis of the graph that you are (probably!!!)
> trying to make.
>
> Instead of just calculating the final number its good to at least once the
> simulation is done to do a sort of quick sanity check to make sure
> everything is in order by making sure you have the right number of frames
> in the trajectory.
>
> Hope this helps.
>
> On Thu, Aug 17, 2017 at 1:31 AM, Saikat Pal <saikatpaliitg_at_remove_yahoo.
> com> wrote:
>
> Dear all,
> I have performed secondary structure analysis using VMD. I have get the
> result. I want to convert frames to nano seconds.What should I do ??