Daniel Cheong wrote:
Hi Mark,
Thanks for all your replies and suggestions! I really appreciate it.
The observations are indeed inconsistent and that is why I am quite
confused. I am not changing anything in my mdp file except for the
energy groups. I literally use the same file and just add/change/remove
the line for the energy group, save the file and run the calculation
again with a different output filename. I don't even touch any of the
cutoff or neighbor list generation frequency or any of the other
parameters. In fact I am not even running any MD on it. I am just
calculating the initial energy of the configuration. Hence my surprise
when I find the total and non-bonded energies turn out different.
Well, start fresh and keep a record of exactly what you do, don't
over-write any files. If you can reproduce this finding in this way,
tar+gz all of that up and put it on a website and someone may look at it
for you.
Mark
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