Fix unwrapping and diffusion imaging for NPT trajectories#1027

Merged

drroe merged 16 commits intoAmber-MD:masterfrom

drroe:check.unwrap.frac

May 10, 2023

Commits on May 9, 2023

Do unwrapping entirely in fractional space to avoid problems unwrapping
Daniel R. Roe
committed
Add dt keyword for dcd trajout to set time step. Ensure time step is
Daniel R. Roe
committed

Commits on May 10, 2023

Use the image list so bymol and byres are honored
Daniel R. Roe
committed
Cannot use push_back in an OpenMP loop
Daniel R. Roe
committed
Fix imaging in diffusion calc for NPT simulations
Daniel R. Roe
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If using a reference structure, ensure frac coords get calcd for it
Daniel R. Roe
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Explicitly make tests byatom
Daniel R. Roe
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Update help
Daniel R. Roe
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Remove the old unwrap routines
Daniel R. Roe
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Remove old Unwrap templates
Daniel R. Roe
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Fix up unwrap manual entry; note that default is actually unwrap by atom
Daniel R. Roe
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Add dt option to dcd trajout
Daniel R. Roe
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6.19.0. Minor version bump for fixed unwrapping and fixed diffusion imaging for
Daniel R. Roe
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Properly read time from charmm dcd. Add t0 and nstep options to charmm
Daniel R. Roe
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Add options to manual. Change t0 to step0
Daniel R. Roe
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Get rid of old unused function definitions
Daniel R. Roe
committed