From e7edcfa4fa50fbaaa374af6fb193bde374ffa8a6 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Wed, 22 Oct 2025 21:23:50 +0100 Subject: [PATCH 01/11] Add release 1.7 blog post --- _posts/2025-10-22-release-v1.7.md | 57 +++++++++++++++++++ assets/images/per_benchmark_presentation.png | Bin 0 -> 27925 bytes 2 files changed, 57 insertions(+) create mode 100644 _posts/2025-10-22-release-v1.7.md create mode 100644 assets/images/per_benchmark_presentation.png diff --git a/_posts/2025-10-22-release-v1.7.md b/_posts/2025-10-22-release-v1.7.md new file mode 100644 index 0000000..195b997 --- /dev/null +++ b/_posts/2025-10-22-release-v1.7.md @@ -0,0 +1,57 @@ +--- +layout: post +title: "OpenFE v1.7: SepTop, ABFEs, faster simulations, and more!" +categories: science update +--- + +We are pleased to release version 1.7 of **openfe**! + +This release brings along some long-awaited features, notably including new Protocols (SepTop & ABFEs), and performance improvements. +Please see below for some highlights, you can find more details on our [changelog][]. + +## New alchemical simulation protocols + +### Separated Topologies + +We include a new relative binding free energy protocol based on the Separated Topologies (SepTop) method, as defined by [Rocklin et al.][] and [Baumann et al.][]. Using SepTop, you can calculate the difference in binding free energy between two ligands by essentially performing two absolute binding free energy calculations simultaneously in opposite directions. Crucially, this avoids the needs for creating a hybrid topology, making atom mapping unnecessary and allowing for scaffold hopping! + +Please see our [SepTop tutorial][] for a demonstration on how to use it! You can also read more about the method in our [SepTop user guide][] entry. + +### Absolute Binding Free Energies + +We also include a new Absolute Binding Free Energy (ABFE) protocol, based on a partial annhilation scheme. This method allows for the direct calculation of binding affinities by alchemically removing a ligand from its binding site. + +Please see our [ABFE tutorial][] and associcated [ABFE user guide entry][] to see how to use the method. + +## Performance improvements through better default settings + +We have updated our default settings to maximize the performance of `openfe`, leading to a ~ 2x performance improvement compared to the v1.0 release! + +The figure below shows the average performance of a single thermodynamic cycle for a pairwise transformation using our relative binding free energy hybrid topology protocol. We see see a drop from ~ 6 hours to ~ 3 hours by switching our default settings and moving to OpenMM 8.2. This can be further improved by layering multiple simulation using the [NVIDIA multi-processing service][] + +average cost of a ligand pair alchemical cycle over the JACS set. + +These settings updates mostly involve moving away from overly conservative parameters to ones that are more widely used in production settings. These include: + * Switching for a cubic to a dodecahedron box for solvation, avoiding excess waters. + * Increasing the replica exchange rate to 2.5 ps (from 1 ps), reducing performance losses linked to GPU context switches. + * Reducing the nonbonded cutoff from 1.0 nm to the OpenFF recommended value of 0.9 nm. + +These new default settings were extensively validated on RBFE and AHFE simulations, showing little to no difference against the previous defaults. + +## Installing `openfe` v1.7.0 + +`openfe` is made available as a [conda-forge][] package, or [docker and singularity images][]. + +Please see our [installation instructions][] for details on how to install `openfe`. + +[Rocklin et al.]: https://doi.org/10.1063/1.4792251 +[Baumann et al.]: https://doi.org/10.1021/acs.jctc.3c00282 +[SepTop tutorial]: https://docs.openfree.energy/en/latest/tutorials/septop_tutorial.html +[SepTop user guide]: https://docs.openfree.energy/en/latest/guide/protocols/septop.html +[ABFE tutorial]: https://docs.openfree.energy/en/latest/tutorials/abfe_tutorial.html +[ABFE user guide entry]: https://docs.openfree.energy/en/latest/guide/protocols/absolutebinding.html +[changelog]: https://docs.openfree.energy/en/latest/CHANGELOG.html +[NVIDIA multi-processing service]: https://developer.nvidia.com/blog/maximizing-openmm-molecular-dynamics-throughput-with-nvidia-multi-process-service/ +[docker and singularity images]: ghcr.io/openfreeenergy/openfe +[conda-forge]: https://anaconda.org/conda-forge/openfe +[installation instructions]: https://docs.openfree.energy/en/latest/installation.html \ No newline at end of file diff --git a/assets/images/per_benchmark_presentation.png b/assets/images/per_benchmark_presentation.png new file mode 100644 index 0000000000000000000000000000000000000000..d0b9debd7a252a84c88ff877daebab9c99a6e37f GIT binary patch literal 27925 zcmd?Rd038Z`!;$f2@Pau&_tnVqCzDVB^o6(NrMKJ=21~14K$D@5*idqn&(MHsT8GA 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zZVTJXFZPmc_JePUI*a1~FWqu=-Nn#3s=l=#4K2@JsqW*Qc`LGJYxU$go9ej_K?G^v;TKD4 z6&WE4Mqm+{H52MZCZ6D})uG} zC3gonqa|xy6?%^dJAh`XbR*vtEXMo4cYXI+Y`z(}ZGm>#6@I7F1l; Date: Wed, 22 Oct 2025 21:34:12 +0100 Subject: [PATCH 02/11] try fix the src entry --- _posts/2025-10-22-release-v1.7.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_posts/2025-10-22-release-v1.7.md b/_posts/2025-10-22-release-v1.7.md index 195b997..daa85b8 100644 --- a/_posts/2025-10-22-release-v1.7.md +++ b/_posts/2025-10-22-release-v1.7.md @@ -29,7 +29,7 @@ We have updated our default settings to maximize the performance of `openfe`, le The figure below shows the average performance of a single thermodynamic cycle for a pairwise transformation using our relative binding free energy hybrid topology protocol. We see see a drop from ~ 6 hours to ~ 3 hours by switching our default settings and moving to OpenMM 8.2. This can be further improved by layering multiple simulation using the [NVIDIA multi-processing service][] -average cost of a ligand pair alchemical cycle over the JACS set. +average cost of a ligand pair alchemical cycle over the JACS set. These settings updates mostly involve moving away from overly conservative parameters to ones that are more widely used in production settings. These include: * Switching for a cubic to a dodecahedron box for solvation, avoiding excess waters. From 50cdf47c4c35d1d2a877bbb8a0bb74e4c66a6b43 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Wed, 22 Oct 2025 22:50:29 +0100 Subject: [PATCH 03/11] Apply suggestion from @atravitz Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com> --- _posts/2025-10-22-release-v1.7.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/_posts/2025-10-22-release-v1.7.md b/_posts/2025-10-22-release-v1.7.md index daa85b8..f36be7a 100644 --- a/_posts/2025-10-22-release-v1.7.md +++ b/_posts/2025-10-22-release-v1.7.md @@ -7,7 +7,8 @@ categories: science update We are pleased to release version 1.7 of **openfe**! This release brings along some long-awaited features, notably including new Protocols (SepTop & ABFEs), and performance improvements. -Please see below for some highlights, you can find more details on our [changelog][]. + +Please see below for some highlights and see the [Changelog][] for more details. ## New alchemical simulation protocols From c8c715a3b7f0757a3c5f351e3b6db292c861fbb7 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Wed, 22 Oct 2025 22:50:41 +0100 Subject: [PATCH 04/11] Apply suggestion from @IAlibay --- _posts/2025-10-22-release-v1.7.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_posts/2025-10-22-release-v1.7.md b/_posts/2025-10-22-release-v1.7.md index f36be7a..ee5fd78 100644 --- a/_posts/2025-10-22-release-v1.7.md +++ b/_posts/2025-10-22-release-v1.7.md @@ -51,7 +51,7 @@ Please see our [installation instructions][] for details on how to install `open [SepTop user guide]: https://docs.openfree.energy/en/latest/guide/protocols/septop.html [ABFE tutorial]: https://docs.openfree.energy/en/latest/tutorials/abfe_tutorial.html [ABFE user guide entry]: https://docs.openfree.energy/en/latest/guide/protocols/absolutebinding.html -[changelog]: https://docs.openfree.energy/en/latest/CHANGELOG.html +[Changelog]: https://docs.openfree.energy/en/latest/CHANGELOG.html [NVIDIA multi-processing service]: https://developer.nvidia.com/blog/maximizing-openmm-molecular-dynamics-throughput-with-nvidia-multi-process-service/ [docker and singularity images]: ghcr.io/openfreeenergy/openfe [conda-forge]: https://anaconda.org/conda-forge/openfe From 65df46b4635b985ee9a48f801b87b377bc022ef1 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Wed, 22 Oct 2025 22:50:58 +0100 Subject: [PATCH 05/11] Apply suggestion from @atravitz Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com> --- _posts/2025-10-22-release-v1.7.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_posts/2025-10-22-release-v1.7.md b/_posts/2025-10-22-release-v1.7.md index ee5fd78..ee26c62 100644 --- a/_posts/2025-10-22-release-v1.7.md +++ b/_posts/2025-10-22-release-v1.7.md @@ -33,7 +33,7 @@ The figure below shows the average performance of a single thermodynamic cycle f average cost of a ligand pair alchemical cycle over the JACS set. These settings updates mostly involve moving away from overly conservative parameters to ones that are more widely used in production settings. These include: - * Switching for a cubic to a dodecahedron box for solvation, avoiding excess waters. + * Switching from a cubic box to a dodecahedron box for solvation, avoiding excess waters. * Increasing the replica exchange rate to 2.5 ps (from 1 ps), reducing performance losses linked to GPU context switches. * Reducing the nonbonded cutoff from 1.0 nm to the OpenFF recommended value of 0.9 nm. From 353583c9316db0f56407196e10fd648ba098eee1 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Wed, 22 Oct 2025 22:51:31 +0100 Subject: [PATCH 06/11] Apply suggestion from @atravitz Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com> --- _posts/2025-10-22-release-v1.7.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_posts/2025-10-22-release-v1.7.md b/_posts/2025-10-22-release-v1.7.md index ee26c62..31cd427 100644 --- a/_posts/2025-10-22-release-v1.7.md +++ b/_posts/2025-10-22-release-v1.7.md @@ -30,7 +30,7 @@ We have updated our default settings to maximize the performance of `openfe`, le The figure below shows the average performance of a single thermodynamic cycle for a pairwise transformation using our relative binding free energy hybrid topology protocol. We see see a drop from ~ 6 hours to ~ 3 hours by switching our default settings and moving to OpenMM 8.2. This can be further improved by layering multiple simulation using the [NVIDIA multi-processing service][] -average cost of a ligand pair alchemical cycle over the JACS set. +
average cost of a ligand pair alchemical cycle over the JACS set.
These settings updates mostly involve moving away from overly conservative parameters to ones that are more widely used in production settings. These include: * Switching from a cubic box to a dodecahedron box for solvation, avoiding excess waters. From b03541f31a8c0c8e309c2a93908a1f10b8838e53 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Wed, 22 Oct 2025 22:51:46 +0100 Subject: [PATCH 07/11] Apply suggestion from @atravitz Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com> --- _posts/2025-10-22-release-v1.7.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_posts/2025-10-22-release-v1.7.md b/_posts/2025-10-22-release-v1.7.md index 31cd427..4f2729d 100644 --- a/_posts/2025-10-22-release-v1.7.md +++ b/_posts/2025-10-22-release-v1.7.md @@ -28,7 +28,7 @@ Please see our [ABFE tutorial][] and associcated [ABFE user guide entry][] to se We have updated our default settings to maximize the performance of `openfe`, leading to a ~ 2x performance improvement compared to the v1.0 release! -The figure below shows the average performance of a single thermodynamic cycle for a pairwise transformation using our relative binding free energy hybrid topology protocol. We see see a drop from ~ 6 hours to ~ 3 hours by switching our default settings and moving to OpenMM 8.2. This can be further improved by layering multiple simulation using the [NVIDIA multi-processing service][] +The figure below shows the average performance of a single thermodynamic cycle for a pairwise transformation using our relative binding free energy hybrid topology protocol. We see see a drop from ~6 hours to ~3 hours by switching our default settings and moving to OpenMM 8.2. This can be further improved by layering multiple simulation using the [NVIDIA multi-processing service][]
average cost of a ligand pair alchemical cycle over the JACS set.
From 1e293da64e76cb4dff0804bdb509cf5ee96717cf Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Wed, 22 Oct 2025 22:51:57 +0100 Subject: [PATCH 08/11] Apply suggestion from @atravitz Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com> --- _posts/2025-10-22-release-v1.7.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_posts/2025-10-22-release-v1.7.md b/_posts/2025-10-22-release-v1.7.md index 4f2729d..ef3b53a 100644 --- a/_posts/2025-10-22-release-v1.7.md +++ b/_posts/2025-10-22-release-v1.7.md @@ -26,7 +26,7 @@ Please see our [ABFE tutorial][] and associcated [ABFE user guide entry][] to se ## Performance improvements through better default settings -We have updated our default settings to maximize the performance of `openfe`, leading to a ~ 2x performance improvement compared to the v1.0 release! +We have updated our default settings to maximize the performance of `openfe`, leading to a **~2x performance improvement compared to the v1.0 release!** The figure below shows the average performance of a single thermodynamic cycle for a pairwise transformation using our relative binding free energy hybrid topology protocol. We see see a drop from ~6 hours to ~3 hours by switching our default settings and moving to OpenMM 8.2. This can be further improved by layering multiple simulation using the [NVIDIA multi-processing service][] From 575ae08f38829c8dc49d7ae7c04019954e039bc0 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Wed, 22 Oct 2025 22:53:43 +0100 Subject: [PATCH 09/11] Apply suggestion from @atravitz Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com> --- _posts/2025-10-22-release-v1.7.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/_posts/2025-10-22-release-v1.7.md b/_posts/2025-10-22-release-v1.7.md index ef3b53a..3e95816 100644 --- a/_posts/2025-10-22-release-v1.7.md +++ b/_posts/2025-10-22-release-v1.7.md @@ -14,7 +14,10 @@ Please see below for some highlights and see the [Changelog][] for more details. ### Separated Topologies -We include a new relative binding free energy protocol based on the Separated Topologies (SepTop) method, as defined by [Rocklin et al.][] and [Baumann et al.][]. Using SepTop, you can calculate the difference in binding free energy between two ligands by essentially performing two absolute binding free energy calculations simultaneously in opposite directions. Crucially, this avoids the needs for creating a hybrid topology, making atom mapping unnecessary and allowing for scaffold hopping! +We include a new relative binding free energy protocol based on the Separated Topologies (SepTop) method, as defined by [Rocklin et al.][] and [Baumann et al.][]. +Using SepTop, you can calculate the difference in binding free energy between two ligands by essentially performing two absolute binding free energy calculations simultaneously in opposite directions. + +Crucially, this avoids the needs for creating a hybrid topology, **making atom mapping unnecessary and allowing for scaffold hopping!** Please see our [SepTop tutorial][] for a demonstration on how to use it! You can also read more about the method in our [SepTop user guide][] entry. From c6568d4f3731fd318300f545bcb7a710ca6ab43e Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Thu, 23 Oct 2025 17:08:30 -0700 Subject: [PATCH 10/11] fix broken link --- _posts/2025-10-22-release-v1.7.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_posts/2025-10-22-release-v1.7.md b/_posts/2025-10-22-release-v1.7.md index 3e95816..83ec63d 100644 --- a/_posts/2025-10-22-release-v1.7.md +++ b/_posts/2025-10-22-release-v1.7.md @@ -56,6 +56,6 @@ Please see our [installation instructions][] for details on how to install `open [ABFE user guide entry]: https://docs.openfree.energy/en/latest/guide/protocols/absolutebinding.html [Changelog]: https://docs.openfree.energy/en/latest/CHANGELOG.html [NVIDIA multi-processing service]: https://developer.nvidia.com/blog/maximizing-openmm-molecular-dynamics-throughput-with-nvidia-multi-process-service/ -[docker and singularity images]: ghcr.io/openfreeenergy/openfe +[docker and singularity images]: https://github.com/OpenFreeEnergy/openfe/pkgs/container/openfe [conda-forge]: https://anaconda.org/conda-forge/openfe [installation instructions]: https://docs.openfree.energy/en/latest/installation.html \ No newline at end of file From 01d3082ef6a0e55ff550c73fa273bbe7d3baf920 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Thu, 23 Oct 2025 17:21:40 -0700 Subject: [PATCH 11/11] formatting --- ...025-10-22-release-v1.7.md => 2025-10-23-release-v1.7.md} | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) rename _posts/{2025-10-22-release-v1.7.md => 2025-10-23-release-v1.7.md} (97%) diff --git a/_posts/2025-10-22-release-v1.7.md b/_posts/2025-10-23-release-v1.7.md similarity index 97% rename from _posts/2025-10-22-release-v1.7.md rename to _posts/2025-10-23-release-v1.7.md index 83ec63d..58c9eb3 100644 --- a/_posts/2025-10-22-release-v1.7.md +++ b/_posts/2025-10-23-release-v1.7.md @@ -4,7 +4,7 @@ title: "OpenFE v1.7: SepTop, ABFEs, faster simulations, and more!" categories: science update --- -We are pleased to release version 1.7 of **openfe**! +We are pleased to announce the release of **openfe** version 1.7.0! This release brings along some long-awaited features, notably including new Protocols (SepTop & ABFEs), and performance improvements. @@ -42,7 +42,7 @@ These settings updates mostly involve moving away from overly conservative param These new default settings were extensively validated on RBFE and AHFE simulations, showing little to no difference against the previous defaults. -## Installing `openfe` v1.7.0 +## Installing `openfe v1.7.0` `openfe` is made available as a [conda-forge][] package, or [docker and singularity images][]. @@ -58,4 +58,4 @@ Please see our [installation instructions][] for details on how to install `open [NVIDIA multi-processing service]: https://developer.nvidia.com/blog/maximizing-openmm-molecular-dynamics-throughput-with-nvidia-multi-process-service/ [docker and singularity images]: https://github.com/OpenFreeEnergy/openfe/pkgs/container/openfe [conda-forge]: https://anaconda.org/conda-forge/openfe -[installation instructions]: https://docs.openfree.energy/en/latest/installation.html \ No newline at end of file +[installation instructions]: https://docs.openfree.energy/en/latest/installation.html