diff --git a/NeuralMD_ODE/MISATO_1000_seed_22/hyperparameter.txt b/NeuralMD_ODE/MISATO_1000_seed_22/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..3a4f00551f29481824a1b0ac2848534662e584fc --- /dev/null +++ b/NeuralMD_ODE/MISATO_1000_seed_22/hyperparameter.txt @@ -0,0 +1 @@ +--seed=22 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --FrameNet_num_radial=100 --num_workers=0 --epochs=100 --batch_size=8 --dataset=MISATO_1000 --NeuralMD_step_size=5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.01 --ODE_method=euler --NeuralMD_binding_model=NeuralMD_Binding01 --no_MLP_velocity --no_NeuralMD_Binding_start_with_first_frame --NeuralMD_Binding_frame_num=10 --output_model_dir=output/MISATO_1000/NeuralMD_Binding01/5_100_0.01_euler_no_NeuralMD_Binding_start_with_first_frame_10_no_MLP_velocity/1e-4_Adam_None_100_8_100_22 diff --git a/NeuralMD_ODE/MISATO_1000_seed_22/model.pth b/NeuralMD_ODE/MISATO_1000_seed_22/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..c9db2c59b7e8798df51c765e01f59167b7f9ccbf --- /dev/null +++ b/NeuralMD_ODE/MISATO_1000_seed_22/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a0e4c1227c82a1a9e2ae29b7392718e3b4d3d665b1c7c3c9637269938ed7d35c +size 8955570 diff --git a/NeuralMD_ODE/MISATO_1000_seed_32/hyperparameter.txt b/NeuralMD_ODE/MISATO_1000_seed_32/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..3b02db2e4b41748c96e4248e099c40960542c3bb --- /dev/null +++ b/NeuralMD_ODE/MISATO_1000_seed_32/hyperparameter.txt @@ -0,0 +1 @@ +--seed=32 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --FrameNet_num_radial=100 --num_workers=0 --epochs=100 --batch_size=8 --dataset=MISATO_1000 --NeuralMD_step_size=5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.01 --ODE_method=euler --NeuralMD_binding_model=NeuralMD_Binding01 --no_MLP_velocity --no_NeuralMD_Binding_start_with_first_frame --NeuralMD_Binding_frame_num=10 --output_model_dir=output/MISATO_1000/NeuralMD_Binding01/5_100_0.01_euler_no_NeuralMD_Binding_start_with_first_frame_10_no_MLP_velocity/1e-4_Adam_None_100_8_100_32 diff --git a/NeuralMD_ODE/MISATO_1000_seed_32/model.pth b/NeuralMD_ODE/MISATO_1000_seed_32/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..02a19ba5a984ff98ca6d15c5dd87ff9171056f62 --- /dev/null +++ b/NeuralMD_ODE/MISATO_1000_seed_32/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:63c3773b8495924ab5161189fc670475a460b096779fa59c72d5297e7b972ef4 +size 8955570 diff --git a/NeuralMD_ODE/MISATO_1000_seed_42/hyperparameter.txt b/NeuralMD_ODE/MISATO_1000_seed_42/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..a3fda0380093144f124c6718214a41588b0424fa --- /dev/null +++ b/NeuralMD_ODE/MISATO_1000_seed_42/hyperparameter.txt @@ -0,0 +1 @@ +--seed=42 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --FrameNet_num_radial=100 --num_workers=0 --epochs=100 --batch_size=8 --dataset=MISATO_1000 --NeuralMD_step_size=5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.01 --ODE_method=euler --NeuralMD_binding_model=NeuralMD_Binding01 --no_MLP_velocity --no_NeuralMD_Binding_start_with_first_frame --NeuralMD_Binding_frame_num=10 --output_model_dir=output/MISATO_1000/NeuralMD_Binding01/5_100_0.01_euler_no_NeuralMD_Binding_start_with_first_frame_10_no_MLP_velocity/1e-4_Adam_None_100_8_100_42 diff --git a/NeuralMD_ODE/MISATO_1000_seed_42/model.pth b/NeuralMD_ODE/MISATO_1000_seed_42/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..c3327d7dc1ea55da052a9249d6f162b4f54aa6d8 --- /dev/null +++ b/NeuralMD_ODE/MISATO_1000_seed_42/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:114e53cfeb6eebfde39a585ff0562e72ef5fc26ebdb345eee30a7be672f1d412 +size 8955570 diff --git a/NeuralMD_ODE/MISATO_100_seed_22/hyperparameter.txt b/NeuralMD_ODE/MISATO_100_seed_22/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..13c040aa2c2d8bcad175ae0e5674f924781af2f5 --- /dev/null +++ b/NeuralMD_ODE/MISATO_100_seed_22/hyperparameter.txt @@ -0,0 +1 @@ +--seed=22 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --FrameNet_num_radial=100 --num_workers=0 --epochs=100 --batch_size=8 --dataset=MISATO_100 --NeuralMD_step_size=5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0 --ODE_method=euler --NeuralMD_binding_model=NeuralMD_Binding01 --no_MLP_velocity --no_NeuralMD_Binding_start_with_first_frame --NeuralMD_Binding_frame_num=20 --output_model_dir=output/MISATO_100/NeuralMD_Binding01/5_100_0_euler_no_NeuralMD_Binding_start_with_first_frame_20_no_MLP_velocity/1e-4_Adam_None_100_8_100_22 diff --git a/NeuralMD_ODE/MISATO_100_seed_22/model.pth b/NeuralMD_ODE/MISATO_100_seed_22/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..31b903afd7b1ad27a811194e821115a3c8730616 --- /dev/null +++ b/NeuralMD_ODE/MISATO_100_seed_22/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:42a7015eef55cb9c53251772ac3a47e1fdbc5f1ca4ba0c2fdff92a232d2c46a9 +size 4813458 diff --git a/NeuralMD_ODE/MISATO_100_seed_32/hyperparameter.txt b/NeuralMD_ODE/MISATO_100_seed_32/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..18c5565f08cccf96033d02c18870f5bf15152056 --- /dev/null +++ b/NeuralMD_ODE/MISATO_100_seed_32/hyperparameter.txt @@ -0,0 +1 @@ +--seed=32 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --FrameNet_num_radial=100 --num_workers=0 --epochs=100 --batch_size=8 --dataset=MISATO_100 --NeuralMD_step_size=5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0 --ODE_method=euler --NeuralMD_binding_model=NeuralMD_Binding01 --no_MLP_velocity --no_NeuralMD_Binding_start_with_first_frame --NeuralMD_Binding_frame_num=20 --output_model_dir=output/MISATO_100/NeuralMD_Binding01/5_100_0_euler_no_NeuralMD_Binding_start_with_first_frame_20_no_MLP_velocity/1e-4_Adam_None_100_8_100_32 diff --git a/NeuralMD_ODE/MISATO_100_seed_32/model.pth b/NeuralMD_ODE/MISATO_100_seed_32/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..e2ed10412df33da3f217740dc86e7650c7a85f3c --- /dev/null +++ b/NeuralMD_ODE/MISATO_100_seed_32/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:9980791c45e521f6116fcec9ecb3508555e7f8b40ed5afb099e8d4a3b71151e0 +size 4813458 diff --git a/NeuralMD_ODE/MISATO_100_seed_42/hyperparameter.txt b/NeuralMD_ODE/MISATO_100_seed_42/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..8ac2557d4b2a54c8ff3d0d251525a281c5aa0d4c --- /dev/null +++ b/NeuralMD_ODE/MISATO_100_seed_42/hyperparameter.txt @@ -0,0 +1 @@ +--seed=42 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --FrameNet_num_radial=100 --num_workers=0 --epochs=100 --batch_size=8 --dataset=MISATO_100 --NeuralMD_step_size=5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0 --ODE_method=euler --NeuralMD_binding_model=NeuralMD_Binding01 --no_MLP_velocity --no_NeuralMD_Binding_start_with_first_frame --NeuralMD_Binding_frame_num=20 --output_model_dir=output/MISATO_100/NeuralMD_Binding01/5_100_0_euler_no_NeuralMD_Binding_start_with_first_frame_20_no_MLP_velocity/1e-4_Adam_None_100_8_100_42 diff --git a/NeuralMD_ODE/MISATO_100_seed_42/model.pth b/NeuralMD_ODE/MISATO_100_seed_42/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..e2291aa1e7eb2a07446073d8fa4437e8eb64c1a4 --- /dev/null +++ b/NeuralMD_ODE/MISATO_100_seed_42/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:364404a7ce61ec1180fa3800c0dcbddf377b672d22f915fc6b19d202710a4a5a +size 4813458 diff --git a/NeuralMD_ODE/MISATO_1KTI_seed_22/hyperparameter.txt b/NeuralMD_ODE/MISATO_1KTI_seed_22/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..9ba80cdc9b85fe5e3f231348165dfffd87d50eda --- /dev/null +++ b/NeuralMD_ODE/MISATO_1KTI_seed_22/hyperparameter.txt @@ -0,0 +1 @@ +--seed=22 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --num_workers=0 --epochs=500 --batch_size=1 --dataset=MISATO --PDB_ID=1KTI --NeuralMD_step_size=0.5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.001 --ODE_method=euler --NeuralMD_window_size=1 --NeuralMD_binding_model=NeuralMD_Binding01 --use_MLP_velocity --FrameNet_num_radial=100 --output_model_dir=output/MISATO_1KTI/NeuralMD_Binding01_AR/0.5_100_0.001_euler_1_100_use_MLP_velocity/1e-4_Adam_None_500_22 diff --git a/NeuralMD_ODE/MISATO_1KTI_seed_22/model.pth b/NeuralMD_ODE/MISATO_1KTI_seed_22/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..b26ef5e743b9c3cb37f23bff5765cc3bc6de6018 --- /dev/null +++ b/NeuralMD_ODE/MISATO_1KTI_seed_22/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e21181a375fd9e7a828d10a0fb4b4739932380d98fda0c1e47280e47b65060a7 +size 13096594 diff --git a/NeuralMD_ODE/MISATO_1KTI_seed_32/hyperparameter.txt b/NeuralMD_ODE/MISATO_1KTI_seed_32/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..b6e08476b7a9003d115f4346cb65007d9b3f6a8b --- /dev/null +++ b/NeuralMD_ODE/MISATO_1KTI_seed_32/hyperparameter.txt @@ -0,0 +1 @@ +--seed=32 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --num_workers=0 --epochs=500 --batch_size=1 --dataset=MISATO --PDB_ID=1KTI --NeuralMD_step_size=0.5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.001 --ODE_method=euler --NeuralMD_window_size=1 --NeuralMD_binding_model=NeuralMD_Binding01 --use_MLP_velocity --FrameNet_num_radial=100 --output_model_dir=output/MISATO_1KTI/NeuralMD_Binding01_AR/0.5_100_0.001_euler_1_100_use_MLP_velocity/1e-4_Adam_None_500_32 diff --git a/NeuralMD_ODE/MISATO_1KTI_seed_32/model.pth b/NeuralMD_ODE/MISATO_1KTI_seed_32/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..d48b80f9d4263950c3b5af41d4ef9d10c4e638e3 --- /dev/null +++ b/NeuralMD_ODE/MISATO_1KTI_seed_32/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8be9164f98ac7ab1e39f7aa882161ed60a18726a802f401ee1a8ab8d696d2890 +size 13096594 diff --git a/NeuralMD_ODE/MISATO_1KTI_seed_42/hyperparameter.txt b/NeuralMD_ODE/MISATO_1KTI_seed_42/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..6a16de15cd83291d853326c657e8cd10015412dd --- /dev/null +++ b/NeuralMD_ODE/MISATO_1KTI_seed_42/hyperparameter.txt @@ -0,0 +1 @@ +--seed=42 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --num_workers=0 --epochs=500 --batch_size=1 --dataset=MISATO --PDB_ID=1KTI --NeuralMD_step_size=0.5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.001 --ODE_method=euler --NeuralMD_window_size=1 --NeuralMD_binding_model=NeuralMD_Binding01 --use_MLP_velocity --FrameNet_num_radial=100 --output_model_dir=output/MISATO_1KTI/NeuralMD_Binding01_AR/0.5_100_0.001_euler_1_100_use_MLP_velocity/1e-4_Adam_None_500_42 diff --git a/NeuralMD_ODE/MISATO_1KTI_seed_42/model.pth b/NeuralMD_ODE/MISATO_1KTI_seed_42/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..52ed3f126e25bc6a1bf970a53a8e641a1aa1f454 --- /dev/null +++ b/NeuralMD_ODE/MISATO_1KTI_seed_42/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ce8a8afd528f361eb4230fc19ea662225601fc971625077466accc52062cbac0 +size 13096594 diff --git a/NeuralMD_ODE/MISATO_1XP6_seed_22/hyperparameter.txt b/NeuralMD_ODE/MISATO_1XP6_seed_22/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..898e824db3bdbc321ae440579137736052e39a2b --- /dev/null +++ b/NeuralMD_ODE/MISATO_1XP6_seed_22/hyperparameter.txt @@ -0,0 +1 @@ +--seed=22 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --num_workers=0 --epochs=500 --batch_size=1 --dataset=MISATO --PDB_ID=1XP6 --NeuralMD_step_size=0.5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.001 --ODE_method=euler --NeuralMD_window_size=1 --NeuralMD_binding_model=NeuralMD_Binding01 --use_MLP_velocity --FrameNet_num_radial=100 --output_model_dir=output/MISATO_1XP6/NeuralMD_Binding01_AR/0.5_100_0.001_euler_1_100_use_MLP_velocity/1e-4_Adam_None_500_22 diff --git a/NeuralMD_ODE/MISATO_1XP6_seed_22/model.pth b/NeuralMD_ODE/MISATO_1XP6_seed_22/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..be92f7d218fdbc186ae1d28340d0cd20d6e482d3 --- /dev/null +++ b/NeuralMD_ODE/MISATO_1XP6_seed_22/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:43a2b6178a0609d36cdf2e4c684c667d13b6c7a3409d1339acbf7010a515df1d +size 13096594 diff --git a/NeuralMD_ODE/MISATO_1XP6_seed_32/hyperparameter.txt b/NeuralMD_ODE/MISATO_1XP6_seed_32/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..b970e41c7cd316e83d1afed1a419c7604c7b5149 --- /dev/null +++ b/NeuralMD_ODE/MISATO_1XP6_seed_32/hyperparameter.txt @@ -0,0 +1 @@ +--seed=32 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --num_workers=0 --epochs=500 --batch_size=1 --dataset=MISATO --PDB_ID=1XP6 --NeuralMD_step_size=0.5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.001 --ODE_method=euler --NeuralMD_window_size=1 --NeuralMD_binding_model=NeuralMD_Binding01 --use_MLP_velocity --FrameNet_num_radial=100 --output_model_dir=output/MISATO_1XP6/NeuralMD_Binding01_AR/0.5_100_0.001_euler_1_100_use_MLP_velocity/1e-4_Adam_None_500_32 diff --git a/NeuralMD_ODE/MISATO_1XP6_seed_32/model.pth b/NeuralMD_ODE/MISATO_1XP6_seed_32/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..d0635576d745525f06b2b8c826b013825a329737 --- /dev/null +++ b/NeuralMD_ODE/MISATO_1XP6_seed_32/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8d87fbf3058579702afcce4322fa2fa5f48123c52f7e919a4b0e82326779a0e6 +size 13096594 diff --git a/NeuralMD_ODE/MISATO_1XP6_seed_42/hyperparameter.txt b/NeuralMD_ODE/MISATO_1XP6_seed_42/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..9c5690276b596a43a02dee870e9fbfaf52137df7 --- /dev/null +++ b/NeuralMD_ODE/MISATO_1XP6_seed_42/hyperparameter.txt @@ -0,0 +1 @@ +--seed=42 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --num_workers=0 --epochs=500 --batch_size=1 --dataset=MISATO --PDB_ID=1XP6 --NeuralMD_step_size=0.5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.001 --ODE_method=euler --NeuralMD_window_size=1 --NeuralMD_binding_model=NeuralMD_Binding01 --use_MLP_velocity --FrameNet_num_radial=100 --output_model_dir=output/MISATO_1XP6/NeuralMD_Binding01_AR/0.5_100_0.001_euler_1_100_use_MLP_velocity/1e-4_Adam_None_500_42 diff --git a/NeuralMD_ODE/MISATO_1XP6_seed_42/model.pth b/NeuralMD_ODE/MISATO_1XP6_seed_42/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..fec0c26ab681d9c4b28104b48e8745a0996b9d36 --- /dev/null +++ b/NeuralMD_ODE/MISATO_1XP6_seed_42/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f2675cb45fe407acf682f26742bf6610124a217adcc6c86ba5b08a79b6e8c46d +size 13096594 diff --git a/NeuralMD_ODE/MISATO_3B9S_seed_22/hyperparameter.txt b/NeuralMD_ODE/MISATO_3B9S_seed_22/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..79400bf6bb4312381a35dfef4c81b25509d8383e --- /dev/null +++ b/NeuralMD_ODE/MISATO_3B9S_seed_22/hyperparameter.txt @@ -0,0 +1 @@ +--seed=22 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --num_workers=0 --epochs=500 --batch_size=1 --dataset=MISATO --PDB_ID=3B9S --NeuralMD_step_size=0.5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.001 --ODE_method=euler --NeuralMD_window_size=1 --NeuralMD_binding_model=NeuralMD_Binding01 --use_MLP_velocity --FrameNet_num_radial=100 --output_model_dir=output/MISATO_3B9S/NeuralMD_Binding01_AR/0.5_100_0.001_euler_1_100_use_MLP_velocity/1e-4_Adam_None_500_22 diff --git a/NeuralMD_ODE/MISATO_3B9S_seed_22/model.pth b/NeuralMD_ODE/MISATO_3B9S_seed_22/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..57649de82191495499cd1b99e5dc70f7dc24a66a --- /dev/null +++ b/NeuralMD_ODE/MISATO_3B9S_seed_22/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f9b4fb132254f8a74d90400a9a153eca7ceb31e656588ed92cc89cc25950e2d8 +size 13096594 diff --git a/NeuralMD_ODE/MISATO_3B9S_seed_32/hyperparameter.txt b/NeuralMD_ODE/MISATO_3B9S_seed_32/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..f38fb8c2160195d0e0e05baa109b2e4748c9266f --- /dev/null +++ b/NeuralMD_ODE/MISATO_3B9S_seed_32/hyperparameter.txt @@ -0,0 +1 @@ +--seed=32 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --num_workers=0 --epochs=500 --batch_size=1 --dataset=MISATO --PDB_ID=3B9S --NeuralMD_step_size=0.5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.001 --ODE_method=euler --NeuralMD_window_size=1 --NeuralMD_binding_model=NeuralMD_Binding01 --use_MLP_velocity --FrameNet_num_radial=100 --output_model_dir=output/MISATO_3B9S/NeuralMD_Binding01_AR/0.5_100_0.001_euler_1_100_use_MLP_velocity/1e-4_Adam_None_500_32 diff --git a/NeuralMD_ODE/MISATO_3B9S_seed_32/model.pth b/NeuralMD_ODE/MISATO_3B9S_seed_32/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..24d1a3f45b0f55cfebcba183527a7696cb4b8ae2 --- /dev/null +++ b/NeuralMD_ODE/MISATO_3B9S_seed_32/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:81985166cbafbd61aae52f5b0285d2e071cb0b09019657c7f8973e78637cd0be +size 13096594 diff --git a/NeuralMD_ODE/MISATO_3B9S_seed_42/hyperparameter.txt b/NeuralMD_ODE/MISATO_3B9S_seed_42/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..807777c161580d155fe43b288f77680bcf26a252 --- /dev/null +++ b/NeuralMD_ODE/MISATO_3B9S_seed_42/hyperparameter.txt @@ -0,0 +1 @@ +--seed=42 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --num_workers=0 --epochs=500 --batch_size=1 --dataset=MISATO --PDB_ID=3B9S --NeuralMD_step_size=0.5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.001 --ODE_method=euler --NeuralMD_window_size=1 --NeuralMD_binding_model=NeuralMD_Binding01 --use_MLP_velocity --FrameNet_num_radial=100 --output_model_dir=output/MISATO_3B9S/NeuralMD_Binding01_AR/0.5_100_0.001_euler_1_100_use_MLP_velocity/1e-4_Adam_None_500_42 diff --git a/NeuralMD_ODE/MISATO_3B9S_seed_42/model.pth b/NeuralMD_ODE/MISATO_3B9S_seed_42/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..3cd9557c529b144dce28dc7b515bcdbdb1b4d524 --- /dev/null +++ b/NeuralMD_ODE/MISATO_3B9S_seed_42/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:73466773328e25a8affc987d723b2d30c3493882c208c08828531c3bbd0b366d +size 13096594 diff --git a/NeuralMD_ODE/MISATO_3EOV_seed_22/hyperparameter.txt b/NeuralMD_ODE/MISATO_3EOV_seed_22/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..1ca9bbbabaf9325e5fd8a2f3a8ec772976882ba3 --- /dev/null +++ b/NeuralMD_ODE/MISATO_3EOV_seed_22/hyperparameter.txt @@ -0,0 +1 @@ +--seed=22 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --num_workers=0 --epochs=500 --batch_size=1 --dataset=MISATO --PDB_ID=3EOV --NeuralMD_step_size=0.5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.001 --ODE_method=euler --NeuralMD_window_size=1 --NeuralMD_binding_model=NeuralMD_Binding01 --use_MLP_velocity --FrameNet_num_radial=100 --output_model_dir=output/MISATO_3EOV/NeuralMD_Binding01_AR/0.5_100_0.001_euler_1_100_use_MLP_velocity/1e-4_Adam_None_500_22 diff --git a/NeuralMD_ODE/MISATO_3EOV_seed_22/model.pth b/NeuralMD_ODE/MISATO_3EOV_seed_22/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..373f860c174730f9a283c5b54855ae5e15f7db80 --- /dev/null +++ b/NeuralMD_ODE/MISATO_3EOV_seed_22/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8baf57099e9d5a2cabe27619364a6089a46d3f9207865a4c64a890b9fa0f27ee +size 13096594 diff --git a/NeuralMD_ODE/MISATO_3EOV_seed_32/hyperparameter.txt b/NeuralMD_ODE/MISATO_3EOV_seed_32/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..32d272352642acef9f08977eccb9ad3636d2b65d --- /dev/null +++ b/NeuralMD_ODE/MISATO_3EOV_seed_32/hyperparameter.txt @@ -0,0 +1 @@ +--seed=32 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --num_workers=0 --epochs=500 --batch_size=1 --dataset=MISATO --PDB_ID=3EOV --NeuralMD_step_size=0.5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.001 --ODE_method=euler --NeuralMD_window_size=1 --NeuralMD_binding_model=NeuralMD_Binding01 --use_MLP_velocity --FrameNet_num_radial=100 --output_model_dir=output/MISATO_3EOV/NeuralMD_Binding01_AR/0.5_100_0.001_euler_1_100_use_MLP_velocity/1e-4_Adam_None_500_32 diff --git a/NeuralMD_ODE/MISATO_3EOV_seed_32/model.pth b/NeuralMD_ODE/MISATO_3EOV_seed_32/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..aef5df3c9291dc40a9ddbeaa7bf46354938e17ce --- /dev/null +++ b/NeuralMD_ODE/MISATO_3EOV_seed_32/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:cbfe1c13c0930ab01f85f0d68aafae91af051d32848c8d768be554c950e35217 +size 13096594 diff --git a/NeuralMD_ODE/MISATO_3EOV_seed_42/hyperparameter.txt b/NeuralMD_ODE/MISATO_3EOV_seed_42/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..eaa2e038c049b238e50006947cee5231e3320e62 --- /dev/null +++ b/NeuralMD_ODE/MISATO_3EOV_seed_42/hyperparameter.txt @@ -0,0 +1 @@ +--seed=42 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --num_workers=0 --epochs=500 --batch_size=1 --dataset=MISATO --PDB_ID=3EOV --NeuralMD_step_size=0.5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.001 --ODE_method=euler --NeuralMD_window_size=1 --NeuralMD_binding_model=NeuralMD_Binding01 --use_MLP_velocity --FrameNet_num_radial=100 --output_model_dir=output/MISATO_3EOV/NeuralMD_Binding01_AR/0.5_100_0.001_euler_1_100_use_MLP_velocity/1e-4_Adam_None_500_42 diff --git a/NeuralMD_ODE/MISATO_3EOV_seed_42/model.pth b/NeuralMD_ODE/MISATO_3EOV_seed_42/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..c19b04765e7f5daabd86bbfb7cf5529d99a427f4 --- /dev/null +++ b/NeuralMD_ODE/MISATO_3EOV_seed_42/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:63e8119be1af10ac927b4a0494841945eb1575c6e0d37428d644e9bb6167c3c4 +size 13096594 diff --git a/NeuralMD_ODE/MISATO_4G3E_seed_22/hyperparameter.txt b/NeuralMD_ODE/MISATO_4G3E_seed_22/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..c6eeb7cf4396731c8c1792f1b5fba09cc83f8eac --- /dev/null +++ b/NeuralMD_ODE/MISATO_4G3E_seed_22/hyperparameter.txt @@ -0,0 +1 @@ +--seed=22 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --num_workers=0 --epochs=500 --batch_size=1 --dataset=MISATO --PDB_ID=4G3E --NeuralMD_step_size=0.5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.001 --ODE_method=euler --NeuralMD_window_size=1 --NeuralMD_binding_model=NeuralMD_Binding01 --use_MLP_velocity --FrameNet_num_radial=100 --output_model_dir=output/MISATO_4G3E/NeuralMD_Binding01_AR/0.5_100_0.001_euler_1_100_use_MLP_velocity/1e-4_Adam_None_500_22 diff --git a/NeuralMD_ODE/MISATO_4G3E_seed_22/model.pth b/NeuralMD_ODE/MISATO_4G3E_seed_22/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..6045bbc9edcb6be3e515fdadec43561a6ab5125e --- /dev/null +++ b/NeuralMD_ODE/MISATO_4G3E_seed_22/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:44943c3ea8b8c8b05abcc8805eec5dd3836d5b5dacdd3d63dd91726d99f86fdb +size 13096594 diff --git a/NeuralMD_ODE/MISATO_4G3E_seed_32/hyperparameter.txt b/NeuralMD_ODE/MISATO_4G3E_seed_32/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..4d572e3afbcec8192b7f31ba6a348660c930b7ec --- /dev/null +++ b/NeuralMD_ODE/MISATO_4G3E_seed_32/hyperparameter.txt @@ -0,0 +1 @@ +--seed=32 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --num_workers=0 --epochs=500 --batch_size=1 --dataset=MISATO --PDB_ID=4G3E --NeuralMD_step_size=0.5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.001 --ODE_method=euler --NeuralMD_window_size=1 --NeuralMD_binding_model=NeuralMD_Binding01 --use_MLP_velocity --FrameNet_num_radial=100 --output_model_dir=output/MISATO_4G3E/NeuralMD_Binding01_AR/0.5_100_0.001_euler_1_100_use_MLP_velocity/1e-4_Adam_None_500_32 diff --git a/NeuralMD_ODE/MISATO_4G3E_seed_32/model.pth b/NeuralMD_ODE/MISATO_4G3E_seed_32/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..87f5c882b4e62471d4176675c012e904f024bd0e --- /dev/null +++ b/NeuralMD_ODE/MISATO_4G3E_seed_32/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:9555be1dabe97b003641c1130aae09a780132314f73dd64c17ca8612f4ad32e7 +size 13096594 diff --git a/NeuralMD_ODE/MISATO_4G3E_seed_42/hyperparameter.txt b/NeuralMD_ODE/MISATO_4G3E_seed_42/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..844004cf11d353700c8d4838aecefb113405486e --- /dev/null +++ b/NeuralMD_ODE/MISATO_4G3E_seed_42/hyperparameter.txt @@ -0,0 +1 @@ +--seed=42 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --num_workers=0 --epochs=500 --batch_size=1 --dataset=MISATO --PDB_ID=4G3E --NeuralMD_step_size=0.5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.001 --ODE_method=euler --NeuralMD_window_size=1 --NeuralMD_binding_model=NeuralMD_Binding01 --use_MLP_velocity --FrameNet_num_radial=100 --output_model_dir=output/MISATO_4G3E/NeuralMD_Binding01_AR/0.5_100_0.001_euler_1_100_use_MLP_velocity/1e-4_Adam_None_500_42 diff --git a/NeuralMD_ODE/MISATO_4G3E_seed_42/model.pth b/NeuralMD_ODE/MISATO_4G3E_seed_42/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..37edf5d3df2a340ead58572cc0659496a28a02be --- /dev/null +++ b/NeuralMD_ODE/MISATO_4G3E_seed_42/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:73f517f9c3829cf271bf1dc3446b1e955e2fbefc68abb003cc6a976924d2ee84 +size 13096594 diff --git a/NeuralMD_ODE/MISATO_4K6W_seed_22/hyperparameter.txt b/NeuralMD_ODE/MISATO_4K6W_seed_22/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..853bb2cef7c73b1ba4cb5b550119ec5286e647c6 --- /dev/null +++ b/NeuralMD_ODE/MISATO_4K6W_seed_22/hyperparameter.txt @@ -0,0 +1 @@ +--seed=22 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --num_workers=0 --epochs=500 --batch_size=1 --dataset=MISATO --PDB_ID=4K6W --NeuralMD_step_size=0.5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.001 --ODE_method=euler --NeuralMD_window_size=1 --NeuralMD_binding_model=NeuralMD_Binding01 --use_MLP_velocity --FrameNet_num_radial=100 --output_model_dir=output/MISATO_4K6W/NeuralMD_Binding01_AR/0.5_100_0.001_euler_1_100_use_MLP_velocity/1e-4_Adam_None_500_22 diff --git a/NeuralMD_ODE/MISATO_4K6W_seed_22/model.pth b/NeuralMD_ODE/MISATO_4K6W_seed_22/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..af0574938656d107062ad0a726ba1d599b114087 --- /dev/null +++ b/NeuralMD_ODE/MISATO_4K6W_seed_22/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:61915d6e5b2ec20ec741927818b8e83549cbcbce145e4c4282f2cb9fdb35362c +size 13096594 diff --git a/NeuralMD_ODE/MISATO_4K6W_seed_32/hyperparameter.txt b/NeuralMD_ODE/MISATO_4K6W_seed_32/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..7b198ef692561d76b4195f514ff901bf25421006 --- /dev/null +++ b/NeuralMD_ODE/MISATO_4K6W_seed_32/hyperparameter.txt @@ -0,0 +1 @@ +--seed=32 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --num_workers=0 --epochs=500 --batch_size=1 --dataset=MISATO --PDB_ID=4K6W --NeuralMD_step_size=0.5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.001 --ODE_method=euler --NeuralMD_window_size=1 --NeuralMD_binding_model=NeuralMD_Binding01 --use_MLP_velocity --FrameNet_num_radial=100 --output_model_dir=output/MISATO_4K6W/NeuralMD_Binding01_AR/0.5_100_0.001_euler_1_100_use_MLP_velocity/1e-4_Adam_None_500_32 diff --git a/NeuralMD_ODE/MISATO_4K6W_seed_32/model.pth b/NeuralMD_ODE/MISATO_4K6W_seed_32/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..244cfd31af833ffa8c46b42a2f9ca3b57f788a8d --- /dev/null +++ b/NeuralMD_ODE/MISATO_4K6W_seed_32/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:9a8d6a738b36910aa34d76ec7c44ae6560b6305e1feeb3a2027d00d34df26bf2 +size 13096594 diff --git a/NeuralMD_ODE/MISATO_4K6W_seed_42/hyperparameter.txt b/NeuralMD_ODE/MISATO_4K6W_seed_42/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..ebc4481a541b90847f357949455d3a68649c0d54 --- /dev/null +++ b/NeuralMD_ODE/MISATO_4K6W_seed_42/hyperparameter.txt @@ -0,0 +1 @@ +--seed=42 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --num_workers=0 --epochs=500 --batch_size=1 --dataset=MISATO --PDB_ID=4K6W --NeuralMD_step_size=0.5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.001 --ODE_method=euler --NeuralMD_window_size=1 --NeuralMD_binding_model=NeuralMD_Binding01 --use_MLP_velocity --FrameNet_num_radial=100 --output_model_dir=output/MISATO_4K6W/NeuralMD_Binding01_AR/0.5_100_0.001_euler_1_100_use_MLP_velocity/1e-4_Adam_None_500_42 diff --git a/NeuralMD_ODE/MISATO_4K6W_seed_42/model.pth b/NeuralMD_ODE/MISATO_4K6W_seed_42/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..08f8fc20da2ae51bc7a631a3dbfe36645800dab9 --- /dev/null +++ b/NeuralMD_ODE/MISATO_4K6W_seed_42/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:fa12e7fc3aed5842df54e033ec51f1ff91f9da20f20ab03d83af8ece04c28d0c +size 13096594 diff --git a/NeuralMD_ODE/MISATO_4YUR_seed_22/hyperparameter.txt b/NeuralMD_ODE/MISATO_4YUR_seed_22/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..13aada48f183edd712bce3adcefb8a19586fa3ef --- /dev/null +++ b/NeuralMD_ODE/MISATO_4YUR_seed_22/hyperparameter.txt @@ -0,0 +1 @@ +--seed=22 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --num_workers=0 --epochs=500 --batch_size=1 --dataset=MISATO --PDB_ID=4YUR --NeuralMD_step_size=0.5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.001 --ODE_method=euler --NeuralMD_window_size=1 --NeuralMD_binding_model=NeuralMD_Binding01 --use_MLP_velocity --FrameNet_num_radial=100 --output_model_dir=output/MISATO_4YUR/NeuralMD_Binding01_AR/0.5_100_0.001_euler_1_100_use_MLP_velocity/1e-4_Adam_None_500_22 diff --git a/NeuralMD_ODE/MISATO_4YUR_seed_22/model.pth b/NeuralMD_ODE/MISATO_4YUR_seed_22/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..cb5d59f968e9c50f1a90adda081494b79e5c991f --- /dev/null +++ b/NeuralMD_ODE/MISATO_4YUR_seed_22/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e7009771614f5e7e596890ce54ccd8f1e9be4db71336f1709b7ce1d057907f02 +size 13096594 diff --git a/NeuralMD_ODE/MISATO_4YUR_seed_32/hyperparameter.txt b/NeuralMD_ODE/MISATO_4YUR_seed_32/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..ff9cb7562fbc5449b8806c0b1f64bdd0884fb8fe --- /dev/null +++ b/NeuralMD_ODE/MISATO_4YUR_seed_32/hyperparameter.txt @@ -0,0 +1 @@ +--seed=32 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --num_workers=0 --epochs=500 --batch_size=1 --dataset=MISATO --PDB_ID=4YUR --NeuralMD_step_size=0.5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.001 --ODE_method=euler --NeuralMD_window_size=1 --NeuralMD_binding_model=NeuralMD_Binding01 --use_MLP_velocity --FrameNet_num_radial=100 --output_model_dir=output/MISATO_4YUR/NeuralMD_Binding01_AR/0.5_100_0.001_euler_1_100_use_MLP_velocity/1e-4_Adam_None_500_32 diff --git a/NeuralMD_ODE/MISATO_4YUR_seed_32/model.pth b/NeuralMD_ODE/MISATO_4YUR_seed_32/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..db0f8769bce5384540be098bf886f56a6cfdf605 --- /dev/null +++ b/NeuralMD_ODE/MISATO_4YUR_seed_32/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a261df2302e833dd335cd497313016d06fe5cc3cda7788bdb9a479cac0b6f547 +size 13096594 diff --git a/NeuralMD_ODE/MISATO_4YUR_seed_42/hyperparameter.txt b/NeuralMD_ODE/MISATO_4YUR_seed_42/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..dfc340060ab213205e75305ea33f9fa9ce2a7570 --- /dev/null +++ b/NeuralMD_ODE/MISATO_4YUR_seed_42/hyperparameter.txt @@ -0,0 +1 @@ +--seed=42 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --num_workers=0 --epochs=500 --batch_size=1 --dataset=MISATO --PDB_ID=4YUR --NeuralMD_step_size=0.5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.001 --ODE_method=euler --NeuralMD_window_size=1 --NeuralMD_binding_model=NeuralMD_Binding01 --use_MLP_velocity --FrameNet_num_radial=100 --output_model_dir=output/MISATO_4YUR/NeuralMD_Binding01_AR/0.5_100_0.001_euler_1_100_use_MLP_velocity/1e-4_Adam_None_500_42 diff --git a/NeuralMD_ODE/MISATO_4YUR_seed_42/model.pth b/NeuralMD_ODE/MISATO_4YUR_seed_42/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..1c61fa41384263ce89bf5937199a3ceae25c1159 --- /dev/null +++ b/NeuralMD_ODE/MISATO_4YUR_seed_42/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4037b24c62f45ccfc196546d6e8eaa879e1c8f934097ce4f78c38b1c52bf3932 +size 13096594 diff --git a/NeuralMD_ODE/MISATO_4ZX0_seed_22/hyperparameter.txt b/NeuralMD_ODE/MISATO_4ZX0_seed_22/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..7543fb1de05675220295e6ec33d3d52f4f845183 --- /dev/null +++ b/NeuralMD_ODE/MISATO_4ZX0_seed_22/hyperparameter.txt @@ -0,0 +1 @@ +--seed=22 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --num_workers=0 --epochs=500 --batch_size=1 --dataset=MISATO --PDB_ID=4ZX0 --NeuralMD_step_size=0.5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.001 --ODE_method=euler --NeuralMD_window_size=1 --NeuralMD_binding_model=NeuralMD_Binding01 --use_MLP_velocity --FrameNet_num_radial=100 --output_model_dir=output/MISATO_4ZX0/NeuralMD_Binding01_AR/0.5_100_0.001_euler_1_100_use_MLP_velocity/1e-4_Adam_None_500_22 diff --git a/NeuralMD_ODE/MISATO_4ZX0_seed_22/model.pth b/NeuralMD_ODE/MISATO_4ZX0_seed_22/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..eccc57c89f3ac6f74a3350a22e87f3bad719f91f --- /dev/null +++ b/NeuralMD_ODE/MISATO_4ZX0_seed_22/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b2ea1f71b19a22e4ec46dee940592208300ec020f7cca472d6fd37cb4e2ee297 +size 13096594 diff --git a/NeuralMD_ODE/MISATO_4ZX0_seed_32/hyperparameter.txt b/NeuralMD_ODE/MISATO_4ZX0_seed_32/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..7d734df5ded62cff27ae7947378f7254f0caebb3 --- /dev/null +++ b/NeuralMD_ODE/MISATO_4ZX0_seed_32/hyperparameter.txt @@ -0,0 +1 @@ +--seed=32 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --num_workers=0 --epochs=500 --batch_size=1 --dataset=MISATO --PDB_ID=4ZX0 --NeuralMD_step_size=0.5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.001 --ODE_method=euler --NeuralMD_window_size=1 --NeuralMD_binding_model=NeuralMD_Binding01 --use_MLP_velocity --FrameNet_num_radial=100 --output_model_dir=output/MISATO_4ZX0/NeuralMD_Binding01_AR/0.5_100_0.001_euler_1_100_use_MLP_velocity/1e-4_Adam_None_500_32 diff --git a/NeuralMD_ODE/MISATO_4ZX0_seed_32/model.pth b/NeuralMD_ODE/MISATO_4ZX0_seed_32/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..1f9c6d30ab184c1867db2c5d40886bfa5ec9df1b --- /dev/null +++ b/NeuralMD_ODE/MISATO_4ZX0_seed_32/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:afb7879f4ad3514989703e05d50ae16f65ca4269480c7094c06ac82d5206639c +size 13096594 diff --git a/NeuralMD_ODE/MISATO_4ZX0_seed_42/hyperparameter.txt b/NeuralMD_ODE/MISATO_4ZX0_seed_42/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..92001b776ade05802227a9c1c58f6fc1d61b0ca9 --- /dev/null +++ b/NeuralMD_ODE/MISATO_4ZX0_seed_42/hyperparameter.txt @@ -0,0 +1 @@ +--seed=42 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --num_workers=0 --epochs=500 --batch_size=1 --dataset=MISATO --PDB_ID=4ZX0 --NeuralMD_step_size=0.5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.001 --ODE_method=euler --NeuralMD_window_size=1 --NeuralMD_binding_model=NeuralMD_Binding01 --use_MLP_velocity --FrameNet_num_radial=100 --output_model_dir=output/MISATO_4ZX0/NeuralMD_Binding01_AR/0.5_100_0.001_euler_1_100_use_MLP_velocity/1e-4_Adam_None_500_42 diff --git a/NeuralMD_ODE/MISATO_4ZX0_seed_42/model.pth b/NeuralMD_ODE/MISATO_4ZX0_seed_42/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..7d693ec6748eb485ec6c098f739fe0d3b39eacc9 --- /dev/null +++ b/NeuralMD_ODE/MISATO_4ZX0_seed_42/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:1245cfd35cc7ab2a6536308a4027e0a588d19fbc85709b623bc167c851c72808 +size 13096594 diff --git a/NeuralMD_ODE/MISATO_5WIJ_seed_22/hyperparameter.txt b/NeuralMD_ODE/MISATO_5WIJ_seed_22/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..560e5b0d6195bdc1e1c0c05e36a832cec61087fd --- /dev/null +++ b/NeuralMD_ODE/MISATO_5WIJ_seed_22/hyperparameter.txt @@ -0,0 +1 @@ +--seed=22 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --num_workers=0 --epochs=500 --batch_size=1 --dataset=MISATO --PDB_ID=5WIJ --NeuralMD_step_size=0.5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.001 --ODE_method=euler --NeuralMD_window_size=1 --NeuralMD_binding_model=NeuralMD_Binding01 --use_MLP_velocity --FrameNet_num_radial=100 --output_model_dir=output/MISATO_5WIJ/NeuralMD_Binding01_AR/0.5_100_0.001_euler_1_100_use_MLP_velocity/1e-4_Adam_None_500_22 diff --git a/NeuralMD_ODE/MISATO_5WIJ_seed_22/model.pth b/NeuralMD_ODE/MISATO_5WIJ_seed_22/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..bc30a9b92bcc1250cad379584ecb26d60ac1e63d --- /dev/null +++ b/NeuralMD_ODE/MISATO_5WIJ_seed_22/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:7d68ee639db46e0ee5d1f94490695fa0bdfb819a0fb84f6882a4482a81757cdf +size 13096594 diff --git a/NeuralMD_ODE/MISATO_5WIJ_seed_32/hyperparameter.txt b/NeuralMD_ODE/MISATO_5WIJ_seed_32/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..72ee17c36f9911e8c8c65ea263b7ffeabbddd17b --- /dev/null +++ b/NeuralMD_ODE/MISATO_5WIJ_seed_32/hyperparameter.txt @@ -0,0 +1 @@ +--seed=32 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --num_workers=0 --epochs=500 --batch_size=1 --dataset=MISATO --PDB_ID=5WIJ --NeuralMD_step_size=0.5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.001 --ODE_method=euler --NeuralMD_window_size=1 --NeuralMD_binding_model=NeuralMD_Binding01 --use_MLP_velocity --FrameNet_num_radial=100 --output_model_dir=output/MISATO_5WIJ/NeuralMD_Binding01_AR/0.5_100_0.001_euler_1_100_use_MLP_velocity/1e-4_Adam_None_500_32 diff --git a/NeuralMD_ODE/MISATO_5WIJ_seed_32/model.pth b/NeuralMD_ODE/MISATO_5WIJ_seed_32/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..f215bb0ecda3c355fa9147c8e7a415c5c98fc7dc --- /dev/null +++ b/NeuralMD_ODE/MISATO_5WIJ_seed_32/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:61b15b53977a69859ca7cfabf3236f52108035732cdeac6a436f3338b2bbbc87 +size 13096594 diff --git a/NeuralMD_ODE/MISATO_5WIJ_seed_42/hyperparameter.txt b/NeuralMD_ODE/MISATO_5WIJ_seed_42/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..1b8dd6990f3d6ab0aeb0ae1ec781a814bbd8c0f1 --- /dev/null +++ b/NeuralMD_ODE/MISATO_5WIJ_seed_42/hyperparameter.txt @@ -0,0 +1 @@ +--seed=42 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --num_workers=0 --epochs=500 --batch_size=1 --dataset=MISATO --PDB_ID=5WIJ --NeuralMD_step_size=0.5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.001 --ODE_method=euler --NeuralMD_window_size=1 --NeuralMD_binding_model=NeuralMD_Binding01 --use_MLP_velocity --FrameNet_num_radial=100 --output_model_dir=output/MISATO_5WIJ/NeuralMD_Binding01_AR/0.5_100_0.001_euler_1_100_use_MLP_velocity/1e-4_Adam_None_500_42 diff --git a/NeuralMD_ODE/MISATO_5WIJ_seed_42/model.pth b/NeuralMD_ODE/MISATO_5WIJ_seed_42/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..c271bd38aa6f222ba307da1d0cfda400446abf1f --- /dev/null +++ b/NeuralMD_ODE/MISATO_5WIJ_seed_42/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:0cc4632e3321dee3a310a7cb45246e8706bf1ffc13546b9bfe27e82f385d113d +size 13096594 diff --git a/NeuralMD_ODE/MISATO_6B7F_seed_22/hyperparameter.txt b/NeuralMD_ODE/MISATO_6B7F_seed_22/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..90849b517934199b82aac2a0a9786af84acbe812 --- /dev/null +++ b/NeuralMD_ODE/MISATO_6B7F_seed_22/hyperparameter.txt @@ -0,0 +1 @@ +--seed=22 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --num_workers=0 --epochs=500 --batch_size=1 --dataset=MISATO --PDB_ID=6B7F --NeuralMD_step_size=0.5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.001 --ODE_method=euler --NeuralMD_window_size=1 --NeuralMD_binding_model=NeuralMD_Binding01 --use_MLP_velocity --FrameNet_num_radial=100 --output_model_dir=output/MISATO_6B7F/NeuralMD_Binding01_AR/0.5_100_0.001_euler_1_100_use_MLP_velocity/1e-4_Adam_None_500_22 diff --git a/NeuralMD_ODE/MISATO_6B7F_seed_22/model.pth b/NeuralMD_ODE/MISATO_6B7F_seed_22/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..83c09e7b05f90c2835624c8cdd14b7bfb634e6e8 --- /dev/null +++ b/NeuralMD_ODE/MISATO_6B7F_seed_22/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b4f580b18b33b01cdc56f0e93cce3520486aaed4704035c98e5a9a416518547a +size 13096594 diff --git a/NeuralMD_ODE/MISATO_6B7F_seed_32/hyperparameter.txt b/NeuralMD_ODE/MISATO_6B7F_seed_32/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..3ec22d67fed4c5176f57dbac12c22d71d6621f34 --- /dev/null +++ b/NeuralMD_ODE/MISATO_6B7F_seed_32/hyperparameter.txt @@ -0,0 +1 @@ +--seed=32 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --num_workers=0 --epochs=500 --batch_size=1 --dataset=MISATO --PDB_ID=6B7F --NeuralMD_step_size=0.5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.001 --ODE_method=euler --NeuralMD_window_size=1 --NeuralMD_binding_model=NeuralMD_Binding01 --use_MLP_velocity --FrameNet_num_radial=100 --output_model_dir=output/MISATO_6B7F/NeuralMD_Binding01_AR/0.5_100_0.001_euler_1_100_use_MLP_velocity/1e-4_Adam_None_500_32 diff --git a/NeuralMD_ODE/MISATO_6B7F_seed_32/model.pth b/NeuralMD_ODE/MISATO_6B7F_seed_32/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..d39cbfb2b6e1a3dfc3ae87c37d208900282f69d2 --- /dev/null +++ b/NeuralMD_ODE/MISATO_6B7F_seed_32/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:df6eb39384650b50b012c433f37b4c96693b48e4792820ac5ff77ef161da7c92 +size 13096594 diff --git a/NeuralMD_ODE/MISATO_6B7F_seed_42/hyperparameter.txt b/NeuralMD_ODE/MISATO_6B7F_seed_42/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..abccf7f41ad79b9217646679044d9a432a631739 --- /dev/null +++ b/NeuralMD_ODE/MISATO_6B7F_seed_42/hyperparameter.txt @@ -0,0 +1 @@ +--seed=42 --lr=1e-4 --optimizer=Adam --lr_scheduler=None --num_workers=0 --epochs=500 --batch_size=1 --dataset=MISATO --PDB_ID=6B7F --NeuralMD_step_size=0.5 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.001 --ODE_method=euler --NeuralMD_window_size=1 --NeuralMD_binding_model=NeuralMD_Binding01 --use_MLP_velocity --FrameNet_num_radial=100 --output_model_dir=output/MISATO_6B7F/NeuralMD_Binding01_AR/0.5_100_0.001_euler_1_100_use_MLP_velocity/1e-4_Adam_None_500_42 diff --git a/NeuralMD_ODE/MISATO_6B7F_seed_42/model.pth b/NeuralMD_ODE/MISATO_6B7F_seed_42/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..6e2a9c10f11c9210cbbc9ed2ba775fb672544eb8 --- /dev/null +++ b/NeuralMD_ODE/MISATO_6B7F_seed_42/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:1f6d6dd773d082e224eb74628723f7c513b6202c68cbfb622bf4108339be386c +size 13096594 diff --git a/NeuralMD_ODE/MISATO_seed_22/hyperparameter.txt b/NeuralMD_ODE/MISATO_seed_22/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..e4699b0c0e0a4ed3170fab406b1277113b847eab --- /dev/null +++ b/NeuralMD_ODE/MISATO_seed_22/hyperparameter.txt @@ -0,0 +1 @@ +--seed=22 --lr=1e-3 --optimizer=Adam --lr_scheduler=None --FrameNet_num_radial=100 --num_workers=0 --epochs=32 --batch_size=8 --dataset=MISATO --NeuralMD_step_size=10 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.000001 --ODE_method=euler --NeuralMD_binding_model=NeuralMD_Binding01 --no_MLP_velocity --no_NeuralMD_Binding_start_with_first_frame --NeuralMD_Binding_frame_num=10 --output_model_dir=output/MISATO/NeuralMD_Binding01/10_100_0.000001_euler_no_NeuralMD_Binding_start_with_first_frame_10_no_MLP_velocity/1e-3_Adam_None_100_8_50_22 diff --git a/NeuralMD_ODE/MISATO_seed_22/model.pth b/NeuralMD_ODE/MISATO_seed_22/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..72e04ce231606a662915ca8df6feda5f6a5a223d --- /dev/null +++ b/NeuralMD_ODE/MISATO_seed_22/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4f35d8fea9a8f38e4f2fb576cf74279a0359a7b614f926b1d453937d7a548351 +size 8955570 diff --git a/NeuralMD_ODE/MISATO_seed_32/hyperparameter.txt b/NeuralMD_ODE/MISATO_seed_32/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..fe3d18907dcfcc0df02aef8b4428ad65beeef69f --- /dev/null +++ b/NeuralMD_ODE/MISATO_seed_32/hyperparameter.txt @@ -0,0 +1 @@ +--seed=32 --lr=1e-3 --optimizer=Adam --lr_scheduler=None --FrameNet_num_radial=100 --num_workers=0 --epochs=32 --batch_size=8 --dataset=MISATO --NeuralMD_step_size=10 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.000001 --ODE_method=euler --NeuralMD_binding_model=NeuralMD_Binding01 --no_MLP_velocity --no_NeuralMD_Binding_start_with_first_frame --NeuralMD_Binding_frame_num=10 --output_model_dir=output/MISATO/NeuralMD_Binding01/10_100_0.000001_euler_no_NeuralMD_Binding_start_with_first_frame_10_no_MLP_velocity/1e-3_Adam_None_100_8_50_32 diff --git a/NeuralMD_ODE/MISATO_seed_32/model.pth b/NeuralMD_ODE/MISATO_seed_32/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..a44b2af67dbcf4077cf246571afc082a630f99c2 --- /dev/null +++ b/NeuralMD_ODE/MISATO_seed_32/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a3cddd5b1f319ad0dc10e88226096380b9a9db291c2333770c3acad04e83bab3 +size 8955570 diff --git a/NeuralMD_ODE/MISATO_seed_42/hyperparameter.txt b/NeuralMD_ODE/MISATO_seed_42/hyperparameter.txt new file mode 100644 index 0000000000000000000000000000000000000000..a68af00702a1a73dbdb183b828c9d256e7b137de --- /dev/null +++ b/NeuralMD_ODE/MISATO_seed_42/hyperparameter.txt @@ -0,0 +1 @@ +--seed=42 --lr=1e-3 --optimizer=Adam --lr_scheduler=None --FrameNet_num_radial=100 --num_workers=0 --epochs=32 --batch_size=8 --dataset=MISATO --NeuralMD_step_size=10 --NeuralMD_scaling=100 --NeuralMD_velocity_refined_value_coefficient=0.000001 --ODE_method=euler --NeuralMD_binding_model=NeuralMD_Binding01 --no_MLP_velocity --no_NeuralMD_Binding_start_with_first_frame --NeuralMD_Binding_frame_num=10 --output_model_dir=output/MISATO/NeuralMD_Binding01/10_100_0.000001_euler_no_NeuralMD_Binding_start_with_first_frame_10_no_MLP_velocity/1e-3_Adam_None_100_8_50_42 diff --git a/NeuralMD_ODE/MISATO_seed_42/model.pth b/NeuralMD_ODE/MISATO_seed_42/model.pth new file mode 100644 index 0000000000000000000000000000000000000000..0479126e5bfdfbbb1c753be001e8177425f72707 --- /dev/null +++ b/NeuralMD_ODE/MISATO_seed_42/model.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a521b9134366c292de6949f4e79c9abc59792f733a34f77dc6630ee402eadbb4 +size 8955570