perhaps I don't understand your problem at all.
But summary_avg.EKTOT file is the average value of all numbers
in summary.EKTOT
In [12]: import numpy as np
In [13]: np.loadtxt('./summary.EKTOT').transpose()[1].mean()
Out[13]: 6352.2708758800009
In [14]: !cat summary_avg.EKTOT
480200.000 6352.2709
if you want to plot, do it with *summary.{...}* files (NOT
*sumarry_avg.{...}* file)
Hai
On Wed, Jan 13, 2016 at 9:09 PM, Wong Li Zhe <Wong.LiZhe.student.imu.edu.my>
wrote:
> 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 - 19:00:04 PST
