73 Commits

Author	SHA1	Message	Date
IAlibay	9546bdbd07	Add some docs	2025-03-10 10:46:24 +00:00
Josh Horton	6b775a2c16	add news, update docs and fix typos	2025-01-16 10:17:50 +00:00
richard gowers	8ee14ed0c5	docs: add crossref to chemicalsystems from RBFE protocol docs	2024-04-15 12:25:45 +01:00
richard gowers	3ed1c55fd8	docs: fixup comment which wasn't commenting itself out ... seems to require a blank line	2024-04-15 11:27:19 +01:00
richard gowers	8e3308dafc	docs: fix a couple of references ... define-rbfe and define-rsfe got merged into a new page shouldn't use relative links in docs to avoid breaks	2024-04-15 11:04:09 +01:00
hannahbaumann	191e511ae3	Add table steps and outputs plain MD guide	2024-04-15 11:08:31 +02:00
hannahbaumann	0b9a2e5144	Add outputs for the plain MD protocol	2024-04-15 10:53:28 +02:00
hannahbaumann	d5b7aee3fa	small fixes	2024-04-15 09:59:23 +02:00
hannahbaumann	41c72ce828	Edit todos	2024-04-15 09:43:37 +02:00
richard gowers	679ff03d78	docs: better forward/reverse convergence picture	2024-04-12 12:36:27 +01:00
richard gowers	abf433fe70	docs: check in pictures for RFE analysis section	2024-04-12 11:05:27 +01:00
richard gowers	d3be3f41d9	docs: add example images of analysis ... reformat analysis from bullet list to table to have images side by side	2024-04-12 10:40:12 +01:00
richard gowers	b01bfe8fa1	docs: highlight importance of mbar overlap matrix in rbfe docs	2024-04-12 09:31:08 +01:00
richard gowers	329431a784	docs: fixup merge snafu	2024-04-09 15:22:57 +01:00
richard gowers	210202b923	Merge branch 'docs_protocol_cycles' into docs_protocol_cycles_results	2024-04-09 15:16:24 +01:00
richard gowers	2d6ad7e5d0	docs: more review comments in RFE analysis docs	2024-04-09 14:16:09 +01:00
Richard Gowers	e413f4a2e9	Apply suggestions from code review ... Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com> Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>	2024-04-09 13:58:59 +01:00
richard gowers	562d13c366	docs: review comments on RFE analysis docs	2024-04-05 11:04:18 +01:00
richard gowers	2c563efafe	docs: better descriptions of standard hrex analysis	2024-04-04 13:06:25 +01:00
hannahbaumann	4aa195f4e2	fix references rel	2024-04-04 14:05:19 +02:00
hannahbaumann	31ce13dc36	small fixes	2024-04-04 14:03:17 +02:00
hannahbaumann	e65cada645	Add MBAR references	2024-04-04 13:51:34 +02:00
hannahbaumann	6219eded69	Add softcore info	2024-04-04 13:44:50 +02:00
hannahbaumann	acbb5d9380	Add description lambda settings absolute	2024-04-03 15:55:28 +02:00
hannahbaumann	d00d2db297	more fixes	2024-04-03 15:48:31 +02:00
hannahbaumann	3c793cfdee	Edits plain MD protocol	2024-04-03 10:34:13 +02:00
hannahbaumann	a89ebd7f1c	Add MBAR and pymbar links	2024-04-03 10:29:35 +02:00
hannahbaumann	a846dc6a80	small fixes	2024-04-02 16:03:44 +02:00
hannahbaumann	2f4f663f4a	small fixes	2024-04-02 15:50:55 +02:00
hannahbaumann	998508fd06	addressing reviews 1	2024-04-02 15:43:51 +02:00
Hannah Baumann	31c7a2859c	Update docs/guide/protocols/absolutesolvation.rst ... Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>	2024-04-02 15:27:56 +02:00
hannahbaumann	cb4b533f8f	clean up plain MD	2024-04-02 14:13:11 +02:00
hannahbaumann	ce34298da6	clean up absolute protocol	2024-04-02 14:11:54 +02:00
hannahbaumann	fb441a1217	small fix relative	2024-04-02 14:03:28 +02:00
hannahbaumann	d15aee71c9	cleaning up relative protocol	2024-04-02 13:56:01 +02:00
richard gowers	1b63383723	docs: RFE protocol, start analysis section	2024-04-01 20:15:12 +01:00
richard gowers	26d692772b	docs: some typo fixes	2024-04-01 20:14:59 +01:00
hannahbaumann	49971e7c1f	small fix 100	2024-03-28 15:04:14 +01:00
hannahbaumann	cd51f37500	more changes	2024-03-28 15:00:39 +01:00
hannahbaumann	32944a7c4c	small fixes	2024-03-28 14:51:45 +01:00
hannahbaumann	65c6dff0f8	change link	2024-03-28 14:47:47 +01:00
hannahbaumann	e398dd5327	Add link integrator	2024-03-28 14:44:43 +01:00
hannahbaumann	7d5c6c7711	change header level	2024-03-28 14:25:47 +01:00
hannahbaumann	cfe3ba3f5f	Add tutorials	2024-03-28 14:22:48 +01:00
hannahbaumann	aa4445b471	small fix	2024-03-28 14:18:19 +01:00
hannahbaumann	d58540d332	Addressing comments AFE	2024-03-28 14:15:20 +01:00
hannahbaumann	8a063a6b85	small fix plain MD	2024-03-28 13:49:17 +01:00
hannahbaumann	036435f8e1	add subsection to MD protocol guide	2024-03-28 13:01:12 +01:00
hannahbaumann	6e86ea1460	change links relative	2024-03-28 12:36:23 +01:00
hannahbaumann	dee8177fbf	first pass relative protocol	2024-03-28 12:13:01 +01:00