You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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