Hi,
You could use mdout_analyzer.py (see the manual for details).
You can also use cpptraj to directly read MDOUT files and write
individual components of the energy, e.g.:
readdata mdout name ENE
list dataset
writedata pe_temp.agr ENE[EPtot] ENE[TEMP]
Hope this helps,
-Dan
On Tue, Feb 5, 2019 at 8:56 AM Keiran Corbett <keirancorbett.gmail.com> wrote:
>
> So I have done an collection of MD runs
> Is it possible to output the following graphs in Amber or by another means.
>
> 1. Is it possible to get a potential energy vs time graph for an
> equilibriation step?
> Where the output is similar to the one below.
>
> (I am able to use process_mdout.perl on my production run just not on the
> equilibrium run)
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -2.4834E+05 1.2376E+01 2.9423E+02 O 12886
> BOND = 1171.2821 ANGLE = 2495.8203 DIHED =
> 10811.7594
> VDWAALS = 19216.5666 EEL = -325706.9651 HBOND =
> 0.0000
> 1-4 VDW = 3752.7524 1-4 EEL = 39914.7362 RESTRAINT =
> 0.0000
>
> 2.
> Is it possible to get Temp vs time and energy vs time for an increase in
> temp step.
>
>
>
>
>
> There graphs in this documents are the kind I am aiming for
>
> http://faculty.uml.edu/vbarsegov/teaching/bioinformatics/lectures/MDSimulationsModified.pdf
>
> Many thanks
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Received on Tue Feb 05 2019 - 09:00:03 PST
