Quick question to anyone,
can you extract energies and forces with g_traj and g_energy and feed them to
WHAM for molecule by molecule or atom by atom PMF determination. If so, how do
I get WHAM to read the extracted enrgies as they are written out. I did read
something about a .pdo file if you have wierdness, that it could be used from
the past?
Explanation: WHAM works fine for my system, and gives nice curves and expected
values, however when I try and do this for say a particular amino acid by hand
the values expected vary. I most likely am just screwing the sums (ive been
using every term including rest) or theres a difference between WHAM and my
means of doing the free energy change? I want to stay uniform.
Any help or suggestions appriciated
Sincerely
Stephan Watkins
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