VMD-L Mailing List

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Thu Aug 17 2017 - 09:15:11 CDT

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
>>
>