From 017c26b5726371f858908fda71231b1b1f4a7b80 Mon Sep 17 00:00:00 2001 From: Marc Schuh Date: Tue, 2 Apr 2024 14:55:41 +0200 Subject: [PATCH] fix minor typos --- docs/moving_from_pymbar3.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/moving_from_pymbar3.rst b/docs/moving_from_pymbar3.rst index ea2012eb..e4304975 100644 --- a/docs/moving_from_pymbar3.rst +++ b/docs/moving_from_pymbar3.rst @@ -131,12 +131,12 @@ Free energy surfaces Previously, ``pymbar`` had a method ``PMF`` that estimated a free energy from a series of umbrella samples using a histogram -approach. This was sematically problematin in two ways. First, the +approach. This was semantically problematic in two ways. First, the term PMF (potential of mean force) is somewhat of an ambiguous term, as the potential of mean force has some dependence on the coordinate system in which the mean force is calculated. Since ``pymbar`` does not calculate free energies by integration of mean force, this caused -some comfusion. To be clearer, we now have renamed the class +some confusion. To be clearer, we now have renamed the class ``FES``, for "free energy surface". The inclusion of a PMF function also created some confusion where some @@ -158,7 +158,7 @@ with the code, please see: :ref:`fes_with_pymbar`. Acceleration ------------ -Previous version of ``pymbar`` include acceleration using explict C++ +Previous version of ``pymbar`` include acceleration using explicit C++ inner loops. The C++ interface has become out of date. ``pymbar`` optimization routines are now accelerated with ``jax``. This provides approximately a 2x speed up when performed on most CPUs, and