Also, I took a brief look at the documentation for Grossfield's program, and it says it expects a harmonic potential of the form (k/2)*(x-x0)^2 — which is different than ndfes. When analyzing a distance-based restraint with that program, the harmonic prefactor that you type into the input file should be twice as large as what appears in the amber disang file. When preparing a ndfes metafile, the harmonic prefactor (for a distance-based restraint) would be the same as what appears in the disang file. Therefore, when you say that you "kept the same biasing constant as I used in WHAM (1/2, corresponding to the Amber disang file).", it makes me wonder if you divided by 2 rather than multiplied by two and/or if you used the same prefactor in both wham and ndfes.
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Received on Thu May 01 2025 - 11:00:02 PDT
