Ok. But my problem is I would like to edit the scale so that I get a better illustration of the 'summary_avg kinetic energy'.
As it appears to be in 1 single line which it doesn't make sense (at least for now) as my MD is still running and I shouldn't expect a straight line.
In fact, it should looks something similar to oscillating graph.
Best regards,
Li Zhe
________________________________________
From: Hai Nguyen <nhai.qn.gmail.com>
Sent: Thursday, 14 January, 2016 10:03 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Kinetic Energy
summary_avg.* file have only a single value (average), so for each file,
you should expect to get a single DOT.
Hai
On Wed, Jan 13, 2016 at 8:25 PM, Wong Li Zhe <Wong.LiZhe.student.imu.edu.my>
wrote:
> 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 - 18:30:05 PST
