[AMBER] Graphs

From: Keiran Corbett <keirancorbett.gmail.com>
Date: Tue, 5 Feb 2019 13:56:06 +0000

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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 05 2019 - 06:00:02 PST
Custom Search