VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Wed Aug 16 2017 - 09:53:19 CDT

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 ??
Please help me.
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 ??
> Please help me.
> Thanks and regards,
> Saikat
> 

-- 
Best,
/A