Using gmx_wham for analysis of NAMD-generated umbrella-sampling

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Brief description of tools/files: NAMD 3.0b2

Dear users,

Is there any way to use gmx_wham to analyze NAMD-generated umbrella-sampling? It generates histogram (dat) and colvars value (traj) files.

Thank you in advance.

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No. gmx wham specifically reads GROMACS file types and formats. You will need different tools, perhaps Alan Grossfield’s WHAM program.

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Thank you for the answer. Alan Grossfield’s WHAM program – this is what I use, but bootstrapping is technically not straightforward there.

Taking advantage of your attention, I’d like to ask one more question: I have windows evenly distributed (0.25A between centers, ordinary US, not replica exchange) with a relatively good overlapping of the histograms, except for the energy barrier region. Is it a good idea to add one more window in the middle of this specific region for better histogram overlapping, or would it make the resulting PMF artifactual?
Thank you again.

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Window spacing and force constants do not have to be uniform.

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