gentoo auto-resync : 21:10:2024 - 04:04:33

12 files changed, 97 insertions, 11 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 216d239bffcc..5680eb7a4d15 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 251eafacf63d..c0e2e17fed77 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -2,6 +2,7 @@ AUX gromacs-2020-pytest.patch 1346 BLAKE2B 4b0b34bf4f46ec1acc3d0088ac11323938ee4
 AUX gromacs-2021-cstdint-include.patch 361 BLAKE2B 98c09c5c82d722fc2fcc320741d8f8ed4f661eed7acd66e72ff1423aa2f0eac316add28f5b2b8b65a3b82c160d36aef6948078d3bad3248ffbd7bd63211980d1 SHA512 decf900c565ad9afed33e9a257a2364b63f0f872a5521dc6de4bdf6c7335e15b1cadaf06041f963573c116f1ffcf289a73d0b482df86740ff0874e0ee598825f
 AUX gromacs-2021-cuda-detection.patch 21849 BLAKE2B 4976321e5f2c5bc9b45feeaa29206d77d04d6148ca910652bd3f7923b6e74b7b10f039b5bcc4430826745f6d64b232c536a8ef75cce61556275942e94945acc0 SHA512 6a1d1f0467d27267d214bc4df95c4b15438fffcae6b84e03763425f869e2551490c0f5e2d28774f9dda2daa07da8b5555617721d46e8b4f067eba2b2b86b353d
 AUX gromacs-2021-musl-stdint.patch 601 BLAKE2B 2e871d22655950ee9b9951229e78bc022f74ce7a8aa8063bafa30e0fd97cd0451e0621ab48f985d813fd5d890c0f2d0c9ced6d4b26d86e9d1f6774c084f169af SHA512 d36497423beb86a26ad011432dd6da7169ae42dc00d15bc90ba14de6ecf5eb3217ac987260dce479e5f92d5f3a40fa28c5eb1b51816a92b6a37745f674581280
+AUX gromacs-9999-Fix-build-with-torch.patch 2090 BLAKE2B aefde1bce2a65653707c8da2732df949d74a06141dd5ba6d26120656cdeeac8b0496a7c837f6f833cd7b82b0e3f6633a56dd40677a7c9db7e1c1bfdc19235ff1 SHA512 8f081544645fb459ed92a5879932b956b91d5f92a97b878bfd03429409e9f3c515c5b8797bacc55382a64f2955300213a61e1f7d3bf8530df7a2839f863cc278
 DIST gromacs-2020.7.tar.gz 29175554 BLAKE2B 98f1aa415946f8eb113febc81105f0c1b0919b96fc3c55a0ab83bf3950ff509b81eade92e645adb0bc2b407df239e20cf3f19828b6e08616437c8693c1fddcc8 SHA512 1d375c44cec38445e56cea252623b5b6c565680268999d4b6c14d6dc38759a27227655b2d29efaab9f9115d3677b446cb555e11cddafa0dc10c4827caaa2477b
 DIST gromacs-2021.7.tar.gz 38028032 BLAKE2B 2dc1b15ca8692ca5cf4ad1c7a266b9e2ced064d34a63cef61fea69e48231dd0310cfd8484d29c56cdb599f795d7655959f40038ac933b46ad2841d57bf2b3646 SHA512 ca478533da3bcb377fda30682660db8eb13beef6456fac6013a1a97ec3be60b5594567412e1e2a31392e484f9a40a22da1f12336f4738cf0422ff4f3e8814609
 DIST gromacs-2022.6.tar.gz 40330705 BLAKE2B fdafbd5b2a92d6022dec3e79e961fef220f1eba42850916e7cb70ef459a8d9c6ebc8c1bbe3c105f5b23161dd5c552ec00505d7c0036649b782cf52c311498743 SHA512 91217394f534ca8f78f73189059712e1c2cd354b658722f23768b12748f7bfaf1a5e95227c5ed1b69c1a9b72c3174e9600a712c157ea2f27156387efb823dd67
@@ -20,13 +21,13 @@ DIST regressiontests-2022.6.tar.gz 48615697 BLAKE2B 566adafbc36d3c1faae322fca9cf
 DIST regressiontests-2023.5.tar.gz 48619605 BLAKE2B f2549a34750c6866f054614a00a3360a09b82306e6bd5e5b848e18cdd3a3fabaac6203c5ca734901019403225dd47e0d662838abe9a1db7d07662f1c745b8e4f SHA512 3ccaf9db7dfba641a5e98ebff3d735cae3f679926aba443ffedec20dd6c85e67f0e9711ebad5dfa8105122d5411f5de6ded1802a7da4ddf0599657832c8c597a
 DIST regressiontests-2024.3.tar.gz 32776961 BLAKE2B 6a74977a396f8e82f7aba7a384cc840275b86d470597a4bbb93e97f1c13cd8fcf6d86ab26bdd4a89464b863954c9ed7dbd49af095e821573845f7bda43c2b90b SHA512 1c4afbbca82c9b9ad371713ef5e7e093ca766f25f6fbda55c79ea1aecb2f0a06bdb042d3c8a86e3d9bf9e8b8091244827dbff544f66037ffa56b0bcb341a9d2c
 DIST regressiontests-2024.tar.gz 48142685 BLAKE2B e24c29c2b534f2fe42e4abc122578ba618279f3182f83be604516e6ee2a34ff037b2604b4cda7a9b7e2ea9fce0a386b3efb7c8aa0cac378d6d8c1595be884c76 SHA512 6c4a847c379603590f618a4da7c691b51bbe180ca9dc59abf885ef8599e1b66758171eb05b7d7709d968f559b209c2fa4cfec8f15cc5d072fafe952567002c2e
-EBUILD gromacs-2020.7-r1.ebuild 9836 BLAKE2B fddaab6e06c3a1da28f0e85f5edf03dea4ba38212e933f71f4d7f9e9efe7c042c140ef38492514b65adc4f38d341aa8ea74db5937ef22b84e0f28b1747560f98 SHA512 c3b521a32c3d0690580dfee163a9c21b016c7b7b696d617d7d5991e36de2610b32fd8f0debb05478e15e3d29c99114eeb7704c95dc13f9ff675d2e81cb1d06fb
-EBUILD gromacs-2021.7-r1.ebuild 10139 BLAKE2B 9611b5c6e0d22255f1faf0f5223cf013ffff2407c3f272f7e0eb932414efc63324cca3fe515fbbbaaa318b14709458d338b18b5c38b87081c1f7fb15ff33b31b SHA512 e0c00ba782790361a354d203327e80820e2c5ef9d4fc1130ece1dc6866303059e505146b8dc18e34d1690e0cd153ac9e6c6015b55e92a047ba96e9a74387301b
-EBUILD gromacs-2022.6.ebuild 9583 BLAKE2B 4700542f3a32bc3055617792d56fa63370438e949efaf073ae3e983f25184ed0f7fbf8a13c777c0da0a0965cfae8ad96625e76ec4d69e5ade60b71d6466fe4af SHA512 9c7c0a0692cd31102c4edce4b33d4e61afb12cf034ad804ba131d40f60cb2b3cf05a424b3f40e4001ea09ee5a5c354b4d98e9a709ee75d5c8d134ee0a579bd09
-EBUILD gromacs-2023.5.ebuild 9738 BLAKE2B af8b9cfb076d9bf0d49544cb5a7b2bcec58ccbfd20a74eb3082e818a890901d10734aa1aba3b1425aab0c0999f16afe83423a865a823e24433703380a8ed5153 SHA512 19a573be8b616440e6680a27ad4a43195d39e265142dad103f6d27d952594c8a99410c98ec2fb8792e7d1318e8a58172b0c53dfc6c494a1662793ea123cdc935
-EBUILD gromacs-2023.9999.ebuild 9738 BLAKE2B af8b9cfb076d9bf0d49544cb5a7b2bcec58ccbfd20a74eb3082e818a890901d10734aa1aba3b1425aab0c0999f16afe83423a865a823e24433703380a8ed5153 SHA512 19a573be8b616440e6680a27ad4a43195d39e265142dad103f6d27d952594c8a99410c98ec2fb8792e7d1318e8a58172b0c53dfc6c494a1662793ea123cdc935
-EBUILD gromacs-2024.3.ebuild 9745 BLAKE2B 254a8fd8fd9b12cdb0afbbd98539add499934781db7a2a249b1fd5dd077227d6a50a23cadb87e409aaf51a7188491dc4662f305142ebc8388b9ef823bbe7b45d SHA512 e9d3a2346f38a64f125bb20031f37e3ffde9c17b50f7812b682818417dc2c68aef0afec206a58f91e5c9af091ce198b97e998ecf6fc5b6c64d861cfda31be755
-EBUILD gromacs-2024.9999.ebuild 9745 BLAKE2B 254a8fd8fd9b12cdb0afbbd98539add499934781db7a2a249b1fd5dd077227d6a50a23cadb87e409aaf51a7188491dc4662f305142ebc8388b9ef823bbe7b45d SHA512 e9d3a2346f38a64f125bb20031f37e3ffde9c17b50f7812b682818417dc2c68aef0afec206a58f91e5c9af091ce198b97e998ecf6fc5b6c64d861cfda31be755
+EBUILD gromacs-2020.7-r1.ebuild 9908 BLAKE2B 71b4d9bfd7def50f1ee99efd1f0355860aa3fb2ac160c4e3e79603d5b20f7f3aedc8cac0ee19b7b94cef310ee27656cd72d207531815735791856550a61a5c8c SHA512 f96a9bdc517356a89b1603e27a209149a3b5944d7b59c87e4318ea67f3c201475a7d263b81f25553935bbcc912d14b4ea276b1ab0962c6743010759bccaeca68
+EBUILD gromacs-2021.7-r1.ebuild 10211 BLAKE2B 93cdfb55a929a999fb261f1f00366bc77b8a6e2bad1233baf85d6dd23291d1574c62f898b8c8ec057aaf911164bbe3c08cdd00a92843040fc02c6521c9849d9b SHA512 022be04a04c5aa8198803941ddb20543961f01b8bd2c9e2901a2c879e15c8b3bba538f429ed50c6b88cf923262398fab304ceb8ee15176aeed5efff5d87f020e
+EBUILD gromacs-2022.6.ebuild 9655 BLAKE2B 3d0e21ae4e04602b390ff7f810c355f5a79a4602e582e4d06103119d21ce3771ebd8ad230f33fd37f786b3e14ce614c949658241a700f75531b8d08077cd97d5 SHA512 9df7661a40d23a3bcec74dd962e021aca7a0a1f5d30ce42bacd4737860e71fb7ef665576079e75d72e7758d3aa3cf5b04a186dba6b02ab9ace90a24ef031bfbd
+EBUILD gromacs-2023.5.ebuild 9810 BLAKE2B 29946a30ec5fc7c19233790c48a8e6657006b5a50fae49c188444a6d03f44e8f80ecbaff12b97041a22dd42e33485a8072859b9b3cca86f198cf0fee691e2b95 SHA512 6ac853da2413ebad69a010b66ff53941fe65fe2bdae5d9aec63de376036388c7dff3017243c528d3175126f118420e2187a48d804eb096440eea3d0d755ffacd
+EBUILD gromacs-2023.9999.ebuild 9810 BLAKE2B 29946a30ec5fc7c19233790c48a8e6657006b5a50fae49c188444a6d03f44e8f80ecbaff12b97041a22dd42e33485a8072859b9b3cca86f198cf0fee691e2b95 SHA512 6ac853da2413ebad69a010b66ff53941fe65fe2bdae5d9aec63de376036388c7dff3017243c528d3175126f118420e2187a48d804eb096440eea3d0d755ffacd
+EBUILD gromacs-2024.3.ebuild 9817 BLAKE2B 65f5ae4402abc5b2b2fac677fb2ca0a62c97ab9c9d7738ca3491d669772a233d65b8e61afa1f441b9b08f1ed31866cb3fed3aa0bd6b76ef894b5f066c7385f7d SHA512 fcc3c48c835590eb96a773981428435e4b048f1a5fbbdc71f8303a89f46257974ed12bfc1649516cb688d8a959f730d4d59dc5555b6982cf7b9fb5595f545a26
+EBUILD gromacs-2024.9999.ebuild 9817 BLAKE2B 65f5ae4402abc5b2b2fac677fb2ca0a62c97ab9c9d7738ca3491d669772a233d65b8e61afa1f441b9b08f1ed31866cb3fed3aa0bd6b76ef894b5f066c7385f7d SHA512 fcc3c48c835590eb96a773981428435e4b048f1a5fbbdc71f8303a89f46257974ed12bfc1649516cb688d8a959f730d4d59dc5555b6982cf7b9fb5595f545a26
 EBUILD gromacs-2024.ebuild 9738 BLAKE2B af8b9cfb076d9bf0d49544cb5a7b2bcec58ccbfd20a74eb3082e818a890901d10734aa1aba3b1425aab0c0999f16afe83423a865a823e24433703380a8ed5153 SHA512 19a573be8b616440e6680a27ad4a43195d39e265142dad103f6d27d952594c8a99410c98ec2fb8792e7d1318e8a58172b0c53dfc6c494a1662793ea123cdc935
-EBUILD gromacs-9999.ebuild 9745 BLAKE2B 254a8fd8fd9b12cdb0afbbd98539add499934781db7a2a249b1fd5dd077227d6a50a23cadb87e409aaf51a7188491dc4662f305142ebc8388b9ef823bbe7b45d SHA512 e9d3a2346f38a64f125bb20031f37e3ffde9c17b50f7812b682818417dc2c68aef0afec206a58f91e5c9af091ce198b97e998ecf6fc5b6c64d861cfda31be755
-MISC metadata.xml 1375 BLAKE2B 321b7db8536061655a6efaa40110f4858633921292eba465b85fe0cb50280842e511f2f11385fe5d62bbdfb40e9c0c76e8e986a1efce8eac25d52c438d7ed5f4 SHA512 cc61e0b477f6576079a0f7910475b9091c1c521fbb48efab365d355e3c0a80cd19e1ea9028cb269d37c2572546b1be66a210512e40ff0f2d6314d1b0138cdba6
+EBUILD gromacs-9999.ebuild 10089 BLAKE2B c141bdd9c2bb7c3fe3dcc4ec8c8d6c22e79809f58f71a1df57b1ef3de5c76378fd8ee660ff667c3ef2ced6160003392e3a2b2b6b17bf71343c62e330a4285062 SHA512 8f9beb4b0f07642b66efcbd62c386bd3795439e940ae0c279958dff629d8387ab32dda49b012de0115ce2bf7f341c90cda3c12046381a63806e013852e3d602c
+MISC metadata.xml 1461 BLAKE2B fa82d5e83fa403fe8c31d076b2cf577d4299b2c97e993b02634c32e8c74088825f8ef61417bc1294947408fddc5b831b983574dafaac5c6975c06af74d890f00 SHA512 ce2b73c332585d9cfb7d1c7cbc49e5fb94f828191c8805463c03e3f215a7137253796ab49718148ea0c5a6ab85b45794b2fe5d213e0d35b2013ea41f6079d484
diff --git a/sci-chemistry/gromacs/files/gromacs-9999-Fix-build-with-torch.patch b/sci-chemistry/gromacs/files/gromacs-9999-Fix-build-with-torch.patch
new file mode 100644
index 000000000000..3a42ba4000ed
--- /dev/null
+++ b/sci-chemistry/gromacs/files/gromacs-9999-Fix-build-with-torch.patch
@@ -0,0 +1,40 @@
+From d997978fc0c644784ed929b0c48e153d5c1f1408 Mon Sep 17 00:00:00 2001
+From: Alexey Shvetsov <alexxyum@gmail.com>
+Date: Sat, 19 Oct 2024 21:22:07 +0300
+Subject: [PATCH] Fix build with torch if non default C{XX}_FLAGS set
+MIME-Version: 1.0
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+
+This should fix build colvars with torch if torch was built with non
+default C{,XX}_FLAGS
+
+Erorr info:
+
+FAILED: src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o
+/usr/bin/x86_64-pc-linux-gnu-g++ -DCOLVARS_TORCH -DGMX_DOUBLE=0 -I/usr/include/torch/csrc/api/include  -O2 -pipe -march=skylake -mtune=skylake -std=c++17 -fPIC "-O2 -pipe -march=skylake -mtune=skylake" -D_GLIBCXX_USE_CXX11_ABI=1 -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -MF src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o.d -o src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-9999/work/gromacs-9999/src/external/colvars/colvar.cpp
+cc1plus: error: argument to ‘-O’ should be a non-negative integer, ‘g’, ‘s’, ‘z’ or ‘fast’
+
+This caused by doubling quoted C{,XX}_FLAGS
+
+Signed-off-by: Alexey Shvetsov <alexxyum@gmail.com>
+---
+ cmake/gmxManageColvars.cmake | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/cmake/gmxManageColvars.cmake b/cmake/gmxManageColvars.cmake
+index 509d56e116..f49c820fa0 100644
+--- a/cmake/gmxManageColvars.cmake
++++ b/cmake/gmxManageColvars.cmake
+@@ -52,7 +52,7 @@ function(gmx_manage_colvars)
+             target_link_libraries(colvars_objlib PRIVATE OpenMP::OpenMP_CXX)
+         endif()
+         if(GMX_TORCH)
+-            target_compile_options(colvars_objlib PRIVATE ${CMAKE_CXX_FLAGS} ${TORCH_CXX_FLAGS})
++            target_compile_options(colvars_objlib PRIVATE ${TORCH_CXX_FLAGS})
+             target_include_directories(colvars_objlib PRIVATE ${TORCH_INCLUDE_DIRS})
+             target_compile_definitions(colvars_objlib PRIVATE -DCOLVARS_TORCH)
+         endif()
+-- 
+2.47.0
+
diff --git a/sci-chemistry/gromacs/gromacs-2020.7-r1.ebuild b/sci-chemistry/gromacs/gromacs-2020.7-r1.ebuild
index fa123d04defb..c93e5baf72ef 100644
--- a/sci-chemistry/gromacs/gromacs-2020.7-r1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2020.7-r1.ebuild
@@ -49,6 +49,10 @@ CDEPEND="
 	blas? ( virtual/blas )
 	cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14:= )
 	opencl? ( virtual/opencl )
+	openmp? (
+		sys-devel/gcc[openmp]
+		sys-devel/clang-runtime[openmp]
+	)
 	fftw? ( sci-libs/fftw:3.0= )
 	hwloc? ( sys-apps/hwloc:= )
 	lapack? ( virtual/lapack )
diff --git a/sci-chemistry/gromacs/gromacs-2021.7-r1.ebuild b/sci-chemistry/gromacs/gromacs-2021.7-r1.ebuild
index 1b82d86998ee..8b99117678ed 100644
--- a/sci-chemistry/gromacs/gromacs-2021.7-r1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2021.7-r1.ebuild
@@ -49,6 +49,10 @@ CDEPEND="
 	blas? ( virtual/blas )
 	cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14:=[profiler] )
 	opencl? ( virtual/opencl )
+	openmp? (
+		sys-devel/gcc[openmp]
+		sys-devel/clang-runtime[openmp]
+	)
 	fftw? ( sci-libs/fftw:3.0= )
 	hwloc? ( sys-apps/hwloc:= )
 	lapack? ( virtual/lapack )
diff --git a/sci-chemistry/gromacs/gromacs-2022.6.ebuild b/sci-chemistry/gromacs/gromacs-2022.6.ebuild
index 8ebb3ae9a8dd..92b1f497c860 100644
--- a/sci-chemistry/gromacs/gromacs-2022.6.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2022.6.ebuild
@@ -45,6 +45,10 @@ CDEPEND="
 	blas? ( virtual/blas )
 	cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] )
 	opencl? ( virtual/opencl )
+	openmp? (
+		sys-devel/gcc[openmp]
+		sys-devel/clang-runtime[openmp]
+	)
 	fftw? ( sci-libs/fftw:3.0= )
 	hwloc? ( sys-apps/hwloc:= )
 	lapack? ( virtual/lapack )
diff --git a/sci-chemistry/gromacs/gromacs-2023.5.ebuild b/sci-chemistry/gromacs/gromacs-2023.5.ebuild
index a3319899d419..4ee08b22a7f0 100644
--- a/sci-chemistry/gromacs/gromacs-2023.5.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2023.5.ebuild
@@ -45,6 +45,10 @@ CDEPEND="
 	blas? ( virtual/blas )
 	cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] )
 	opencl? ( virtual/opencl )
+	openmp? (
+		sys-devel/gcc[openmp]
+		sys-devel/clang-runtime[openmp]
+	)
 	fftw? ( sci-libs/fftw:3.0= )
 	hwloc? ( sys-apps/hwloc:= )
 	lapack? ( virtual/lapack )
diff --git a/sci-chemistry/gromacs/gromacs-2023.9999.ebuild b/sci-chemistry/gromacs/gromacs-2023.9999.ebuild
index a3319899d419..4ee08b22a7f0 100644
--- a/sci-chemistry/gromacs/gromacs-2023.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2023.9999.ebuild
@@ -45,6 +45,10 @@ CDEPEND="
 	blas? ( virtual/blas )
 	cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] )
 	opencl? ( virtual/opencl )
+	openmp? (
+		sys-devel/gcc[openmp]
+		sys-devel/clang-runtime[openmp]
+	)
 	fftw? ( sci-libs/fftw:3.0= )
 	hwloc? ( sys-apps/hwloc:= )
 	lapack? ( virtual/lapack )
diff --git a/sci-chemistry/gromacs/gromacs-2024.3.ebuild b/sci-chemistry/gromacs/gromacs-2024.3.ebuild
index 33e343e23e7c..2101629ebc36 100644
--- a/sci-chemistry/gromacs/gromacs-2024.3.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2024.3.ebuild
@@ -45,6 +45,10 @@ CDEPEND="
 	blas? ( virtual/blas )
 	cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] )
 	opencl? ( virtual/opencl )
+	openmp? (
+		sys-devel/gcc[openmp]
+		sys-devel/clang-runtime[openmp]
+	)
 	fftw? ( sci-libs/fftw:3.0= )
 	hwloc? ( sys-apps/hwloc:= )
 	lapack? ( virtual/lapack )
diff --git a/sci-chemistry/gromacs/gromacs-2024.9999.ebuild b/sci-chemistry/gromacs/gromacs-2024.9999.ebuild
index 33e343e23e7c..2101629ebc36 100644
--- a/sci-chemistry/gromacs/gromacs-2024.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2024.9999.ebuild
@@ -45,6 +45,10 @@ CDEPEND="
 	blas? ( virtual/blas )
 	cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] )
 	opencl? ( virtual/opencl )
+	openmp? (
+		sys-devel/gcc[openmp]
+		sys-devel/clang-runtime[openmp]
+	)
 	fftw? ( sci-libs/fftw:3.0= )
 	hwloc? ( sys-apps/hwloc:= )
 	lapack? ( virtual/lapack )
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 33e343e23e7c..9de42117f102 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -18,7 +18,7 @@ if [[ ${PV} = *9999* ]]; then
 		https://gitlab.com/gromacs/gromacs.git
 		https://github.com/gromacs/gromacs.git
 		"
-	[[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
+	[[ ${PV} = 9999 ]] && EGIT_BRANCH="main" || EGIT_BRANCH="release-${PV:0:4}"
 	inherit git-r3
 else
 	SRC_URI="
@@ -39,17 +39,23 @@ HOMEPAGE="https://www.gromacs.org/"
 #        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
 SLOT="0/${PV}"
-IUSE="blas clang clang-cuda cuda  +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
+IUSE="blas clang clang-cuda cuda  +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hdf5 +hwloc lapack mkl mpi nnpot +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
 
 CDEPEND="
 	blas? ( virtual/blas )
 	cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] )
 	opencl? ( virtual/opencl )
+	openmp? (
+		sys-devel/gcc[openmp]
+		sys-devel/clang-runtime[openmp]
+	)
 	fftw? ( sci-libs/fftw:3.0= )
+	hdf5? ( sci-libs/hdf5 )
 	hwloc? ( sys-apps/hwloc:= )
 	lapack? ( virtual/lapack )
 	mkl? ( sci-libs/mkl )
 	mpi? ( virtual/mpi[cxx] )
+	nnpot? ( sci-libs/caffe2[cuda=,opencl=] )
 	sci-libs/lmfit:=
 	>=dev-cpp/muParser-2.3:=
 	${PYTHON_DEPS}
@@ -88,6 +94,8 @@ DOCS=( AUTHORS README )
 
 RESTRICT="!test? ( test )"
 
+PATCHES=( "${FILESDIR}/${P}-Fix-build-with-torch.patch" )
+
 if [[ ${PV} != *9999 ]]; then
 	S="${WORKDIR}/${PN}-${PV/_/-}"
 fi
@@ -178,6 +186,11 @@ src_prepare() {
 src_configure() {
 	local mycmakeargs_pre=( ) extra fft_opts=( )
 	local acce="AUTO"
+	local nnpot="OFF"
+
+	if use nnpot; then
+		nnpot="TORCH"
+	fi
 
 	if use custom-cflags; then
 		#go from slowest to fastest acceleration
@@ -225,9 +238,12 @@ src_configure() {
 		-DGMX_COOL_QUOTES=$(usex offensive)
 		-DGMX_USE_TNG=$(usex tng)
 		-DGMX_BUILD_MANUAL=$(usex build-manual)
+		-DGMX_USE_HDF5=$(usex hdf5)
 		-DGMX_HWLOC=$(usex hwloc)
 		-DGMX_DEFAULT_SUFFIX=off
+		-DGMX_BUILD_HELP=on
 		-DGMX_SIMD="$acce"
+		-DGMX_NNPOT="$nnpot"
 		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
 		-DBUILD_TESTING=$(usex test)
 		-DGMX_BUILD_UNITTESTS=$(usex test)
diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 44ddb19d1d9d..518711308a02 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -19,6 +19,7 @@
 		<flag name="gmxapi-legacy">Enable installing lagacy headers</flag>
 		<flag name="hwloc">Enable HWLoc lib support</flag>
 		<flag name="lmfit">Use external <pkg>sci-libs/lmfit</pkg></flag>
+		<flag name="nnpot">Allow to use <pkg>sci-libs/caffe2</pkg> for NN Potentials</flag>
 		<flag name="opencl">Enable opencl non-bonded kernels</flag>
 		<flag name="single-precision">Single precision version of gromacs (default)</flag>
 		<flag name="tng">Enable new trajectory format - tng</flag>