Hi Jason,
Thanks for your reply.
Yes, I process all the 'output' files using 'process_mdout.perl'.
I am actually trying to plot all the 'summary_avg' file by combining all three of them (potential, kinetic and total) as what illustrated in tutorial B1 section 5.
It is however, the line indicating kinetic energy doesn't make sense as it turns out to be in 1 straight line.
I then re-plot the 'summary_avg' for kinetic energy separately and it does make sense now (fluctuating line graph instead of 1 straight line).
Been trying to adjust the scale so that I don't get a straight line but outcome still the same.
Best regards,
Li Zhe
________________________________________
From: Jason Swails <jason.swails.gmail.com>
Sent: Thursday, 14 January, 2016 8:42 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Kinetic Energy
On Wed, Jan 13, 2016 at 6:54 PM, Wong Li Zhe <Wong.LiZhe.student.imu.edu.my>
wrote:
> Dear all,
>
>
> I am having problem with plotting the 'summary_avg Kinetic energy' graph,
> especially when I combine the potential and total energy.
Why would you combine these two? Kinetic and potential combine to give
total... potential and total don't combine to give anything (except that
total - potential = kinetic).
>
> It is however when I plot the kinetic graph individually, I managed to get
> it in a more meaningful presentation.
>
> Been trying to adjust the scales and etc. but it still looks the same.
>
> Would anyone be able to enlighten me on that?
>
I'm completely lost on what you are even trying to do. What did you do?
What commands did you run? What are you trying to see? What are you
actually seeing?
From the sound of it, you're trying to use process_mdout.perl? Then
plotting some of the data (but how)?
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Jan 13 2016 - 17:30:03 PST
