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 - 06:00:02 PST
