[gmx-users] Re: WHAM question

[lloyd riggs]

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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