You may want to try mdout_analyzer.py instead. Another alternative is
to extract specific terms using cpptraj:
readdata mdout name MyOutput
list datasets
writedata Pressure.agr MyOutput[PRESS]
writedata Density.agr MyOutput[Density]
etc.
-Dan
On Fri, Oct 21, 2016 at 5:52 AM, Ruth Helena Tichauer <rhtichau.laas.fr> wrote:
> Hello,
>
> I had reported it few months ago: the process_mdout.perl script fails (for my mdout files issued with Amber12) in retrieving the density of the system and its volume. Emilio sent me an other version of it but it still isn’t working with my mdout files for both density and volume.
>
> For the test cases, it only fails to extract the density so when you plot it with xmgrace, you get a diagonal such as the one you sent because it is plotting the time against the time.. I guess then, mainly a fix for the density retrieving is needed.
>
> Anyway, find the version of the script Emilio sent me in attachments.
>
> Good luck!
>
> Ruth
>
>
>
>
>> On 19 Oct 2016, at 13:54, David A Case <david.case.rutgers.edu> wrote:
>>
>> On Wed, Oct 19, 2016, Saman Yousuf ali wrote:
>>
>>> Dear All,I have run 70 ps heating step to equilibrate my system before
>>> moving on to running any production MD simulations. After that, I
>>> analyzed output of heating steps. I have followed this tutorial for
>>> plotting http://ambermd.org/tutorials/basic/tutorial3/section6.htm. The
>>> volume, density and pressure graph of my analysis is weird. I don’t
>>> understand the reason. I have attached images here.
>>
>> Please examine the mdout files, and make the plots yourself. Surely the
>> system volume is not zero at zero time, etc. It is possible that there is
>> something now wrong with the process_mdout.perl script: this has been
>> suggested in earlier posts, but I don't remember that anyone has followed up
>> on that.
>>
>> ...dac
>>
>>
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>
>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Fri Oct 21 2016 - 08:00:03 PDT
