Upload 2aa_config.yaml

2aa_config.yaml

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+dataset: 2AA-1-big
+model_config:
+  model_type: custom_attention_transformer_nvp
+  transformer_cvae_config: null
+  transformer_nvp_config: null
+  custom_transformer_nvp_config:
+    atom_embedding_dim: 64
+    latent_mlp_hidden_dims:
+    - 256
+    num_coupling_layers: 12
+    num_transformer_layers: 6
+    encoder_layer_config:
+      d_model: 128
+      dim_feedforward: 2048
+      dropout: 0.0
+      num_heads: 6
+      attention_type: kernel
+      lengthscales:
+      - 0.1
+      - 0.2
+      - 0.5
+      - 0.7
+      - 1.0
+      - 1.2
+      max_radius: null
+      normalise_kernel_values: true
+      cheb_order: null
+      force_asymptotic_zero: null
+    position_layer_index_mod_2: 0
+    conditional_flow_density:
+      scale_requires_grad: true
+      ignore_conditional_velocity: true
+      use_displacement_as_target: true
+  equivariant_nvp_config: null
+  gaussian_density_transformer_config: null
+  graphormer_nvp_config: null
+step_width: 1000000
+batch_size: 256
+num_epochs: 100000000
+patience: 100
+data_augmentation: true
+measure_equivariance_discrepancy: false
+use_aml_logging: false
+loss:
+  nll: null
+  nll_and_energy: null
+  nll_and_acceptance:
+    openmm_provider:
+      pdb_dirs: /mnt/simulated-data/trajectory-data/2AA-1-large
+      device: cpu
+      cache_size: 8
+    random_velocs: true
+    beta: 0.1
+    clamp: false
+    num_samples: 1
+    weights:
+    - 0.9
+    - 0.1
+    pre_softmax_weights: null
+loss_schedule: null
+run_prefix: ''
+optimizer: Lamb
+learning_rate: 1.0e-05
+warmup_steps: 1000
+weight_decay: 0.0
+clip_grad_norm: 100.0
+seed: 0
+randomise_seed: true
+data_dir: /mnt/lmdb-simulated-data/trajectory-data/2AA-1-big/step_width_1000000
+dataset_cache_dir: .data
+dataset_use_lmdb: true
+pdb_dir: /mnt/simulated-data/trajectory-data/2AA-1-large
+output_folder: /mnt/output/projects/timewarp/amlt-results/7328294309.72749-b6024015-4a4c-4fb3-92d3-f4b6ff86975a
+enable_profiler: false
+saved_model_path: /mnt/default/projects/timewarp/amlt-results/7329812703.49702-998fb2c0-84c9-4ee6-b8be-cbe29511a372
+valid_batch_size: 256
+min_check_point_iters: 500
+random_velocities: true
+warm_start: true
+num_pdbs_per_local_batch: 4
+equal_data_spacing: false
+run_valid_first: false
+lr_scheduler:
+  type: plateau
+  factor: 0.5
+  iteration_patience: 10000
+  logging_period: 100
+  alpha: 0.2