Skip to content

Release v2.4.13

Choose a tag to compare

@github-actions github-actions released this 14 May 19:46
· 25 commits to main since this release
  • behavior change: make_membrane_system no longer silently turns on NAMD's on-the-fly pressureProfile calculation during NPT/NPAT bilayer-relaxation stages on CPU NAMD; pressure profile calculation is now opt-in via a new top-level make_membrane_system.compute_pressure_profile block (enabled: false default, plus slabs / freq knobs that map to pressureProfileSlabs / pressureProfileFreq); previously, any NPT/NPAT stage whose other_parameters did not explicitly mention pressureProfile had it auto-injected as on on CPU builds, surprising GPU users (the processor-type guard correctly skipped injection on GPU but the opt-out default was hostile and unintuitive); the mdplot task's profiles=['pressure'] list, which was unconditionally requested by equilibrate_bilayer, is now likewise gated on the new flag so no spurious pressure-profile plotting is attempted when the data is not produced
  • new feature: make_membrane_system now hard-errors with PestiferBuildError if compute_pressure_profile.enabled: true is set under GPU NAMD (processor-type: gpu), or if any explicit other_parameters.pressureProfile setting in a stage is truthy on GPU; CUDA-enabled NAMD does not support pressureProfile, and the previous silent-strip behavior masked user misconfiguration; the error message names the offending stage's ensemble and points at the two ways to fix the conflict (disable the flag, or use a CPU NAMD build)
  • doc: ex16 and ex17 example YAMLs (membrane-embedded HIV-1 gp41 MPER-TM trimer builds) now carry a header comment explaining that their post-equilibration NPAT stage and packaged production run use pressureProfile, so they must be run with a CPU NAMD build; the comment names the specific other_parameters blocks to strip if a user wants to run them on GPU