VMD-L Mailing List

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Thu Aug 17 2017 - 09:32:19 CDT

Hi Ashar,

Do you know of any way to get the Timeline plugin to display the time
instead of the frames? I guess that's what the point of the post is. I
don't use Timeline too much, but I do remember trying (and failing) to get
the Timeline plugin to do the conversion.

On Thu, Aug 17, 2017 at 10:27 AM, Ashar Malik <asharjm_at_gmail.com> wrote:

> Please refer to my earlier message to work out the necessary details.
> Once you have your answer, which would be in femto seconds convert that
> into nano seconds.
> You should be able to do this conversion.
>
> On Fri, Aug 18, 2017 at 2:15 AM, Chitrak Gupta <chgupta_at_mix.wvu.edu>
> wrote:
>
>> Let me guess. Is your problem about the output of the Timeline plugin? If
>> that is the case, you should have mentioned this because people in the
>> forum are not being able to understand your concern. If not, then you would
>> need to go back to the basics of MD simulation.
>>
>> On Thu, Aug 17, 2017 at 8:58 AM, Ashar Malik <asharjm_at_gmail.com> wrote:
>>
>>> 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 ??
>>>> 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
>>>>
>>>
>>
>
>
> --
> Best,
> /A
>