Add configs for ALDP

Author: plainerman

configs/aldp_diagonal_single_gaussian.yaml

@@ -11,18 +11,20 @@ temperature: 300
 gamma: 1.0
 
 num_gaussians: 1
-trainable_weights: False
-base_sigma: 1e-4
+trainable_weights: True
+base_sigma: 1e-5
+internal_coordinates: False
 
-hidden_layers: 256 256 256 256 256 256 256
+hidden_layers: 256 256 256 256 256
 activation: relu
 resnet: True
 
-epochs: 50
+epochs: 150000
 BS: 256
 force_clip: 1e7
 
-num_paths: 256
+num_paths: 1000
 dt: 1e-3
 
-log_plots: True
+log_plots: True
+extension: png

configs/aldp_diagonal_single_gaussian_internal.yaml

@@ -0,0 +1,30 @@
+save_dir: ./out/aldp_diagonal_single_gaussian_internal
+
+start: ./files/AD_A.pdb
+target: ./files/AD_B.pdb
+cv: phi_psi
+
+ode: second_order
+parameterization: diagonal
+T: 1.0
+temperature: 300
+gamma: 1.0
+
+num_gaussians: 1
+trainable_weights: False
+base_sigma: 1e-5
+internal_coordinates: True
+
+hidden_layers: 256 256 256 256 256
+activation: relu
+resnet: True
+
+epochs: 200000
+BS: 256
+force_clip: 1e7
+
+num_paths: 1000
+dt: 1e-3
+
+log_plots: True
+extension: png

configs/aldp_diagonal_two_gaussian.yml

@@ -0,0 +1,30 @@
+save_dir: ./out/aldp_diagonal_two_gaussian
+
+start: ./files/AD_A.pdb
+target: ./files/AD_B.pdb
+cv: phi_psi
+
+ode: second_order
+parameterization: diagonal
+T: 1.0
+temperature: 300
+gamma: 1.0
+
+num_gaussians: 2
+trainable_weights: False
+base_sigma: 1e-4
+internal_coordinates: False
+
+hidden_layers: 256 256 256 256 256 256 256
+activation: relu
+resnet: True
+
+epochs: 200000
+BS: 256
+force_clip: 1e7
+
+num_paths: 1000
+dt: 1e-3
+
+log_plots: True
+extension: png

configs/aldp_diagonal_two_gaussian_internal.yml

@@ -0,0 +1,30 @@
+save_dir: ./out/aldp_diagonal_two_gaussian_internal
+
+start: ./files/AD_A.pdb
+target: ./files/AD_B.pdb
+cv: phi_psi
+
+ode: second_order
+parameterization: diagonal
+T: 1.0
+temperature: 300
+gamma: 1.0
+
+num_gaussians: 2
+trainable_weights: True
+base_sigma: 1e-5
+internal_coordinates: True
+
+hidden_layers: 256 256 256 256 256 256 256
+activation: relu
+resnet: True
+
+epochs: 200000
+BS: 256
+force_clip: 1e7
+
+num_paths: 1000
+dt: 1e-3
+
+log_plots: True
+extension: png