[gmx-users] Re: WHAM question
lloyd.riggs at gmx.ch
Tue Mar 27 16:45:55 CEST 2012
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
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