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gmvae_update

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 Once a suitable set of training hyperparameters has been determined (excluding K and z), perform a systematic grid search to identify the optimal latent-space dimension and number of clusters. Once a suitable set of training hyperparameters has been determined (excluding K and z), perform a systematic grid search to identify the optimal latent-space dimension and number of clusters.
-<code>+
 **Example** **Example**
 +<code>
 python gmvae_pipeline_v2.py --mode grid \ python gmvae_pipeline_v2.py --mode grid \
   --pdb /home/mhsieh/scratch/bst2/orf7a-cov-2_bst2_short/aa/c2_r1_cg2aa/openmm/ca_dcd/ca.pdb \   --pdb /home/mhsieh/scratch/bst2/orf7a-cov-2_bst2_short/aa/c2_r1_cg2aa/openmm/ca_dcd/ca.pdb \
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 Systems       # of     # of   Latent   # of     Batch           Kernel   Learning   # of        Pooling Systems       # of     # of   Latent   # of     Batch           Kernel   Learning   # of        Pooling
              layers   neurons  dim.  clusters size Temp. size rate   filters sizes     Ref              layers   neurons  dim.  clusters size Temp. size rate   filters sizes     Ref
-Trp-cage 2 64 5 8 5000 0.1 [3,3]   0.001   [64,64] [1,1]    J. Chem. Phys. 155, 194108 (2021) doi: 10.1063/5.0069708 +Trp-cage 2 64 5 8 5000 0.1 [3,3]   0.001   [64,64] [1,1]    J. Chem. Phys. (2021) 155, 194108  doi: 10.1063/5.0069708 
-BBA         2 64 6 9 5000 0.1 [3,3]   0.001   [64,64] [2,2]    J. Chem. Phys. 155, 194108 (2021) doi: 10.1063/5.0069708 +BBA         2 64 6 9 5000 0.1 [3,3]   0.001   [64,64] [2,2]    J. Chem. Phys. (2021) 155, 194108  doi: 10.1063/5.0069708 
-villin         3 64 5 6 2500 0.05 [3,3,3]   0.001   [64,64,32] [2,2,1]    J. Chem. Phys. 155, 194108 (2021) doi: 10.1063/5.0069708 +villin         3 64 5 6 2500 0.05 [3,3,3]   0.001   [64,64,32] [2,2,1]    J. Chem. Phys. (2021) 155, 194108  doi: 10.1063/5.0069708 
-BST-2/ORF7a 3 64 5 9 2500 0.05 [3,3,3]   0.001   [64,64,32] [2,2,1]    BBA Biomembranes (2023)1865 (6): 184174. doi: 10.1016/j.bbamem.2023.184174.  +BST-2/ORF7a 3 64 5 9 2500 0.05 [3,3,3]   0.001   [64,64,32] [2,2,1]    BBA Biomembranes (2023) 1865(6), 184174. doi: 10.1016/j.bbamem.2023.184174 
-BST-2/ORF7a 3 64 5 13 2500 0.05 [3,3,3]   0.001   [64,64,32] [2,2,1]    BBA Biomembranes (2023)1865 (6): 184174. doi: 10.1016/j.bbamem.2023.184174.  +BST-2/ORF7a 3 64 5 13 2500 0.05 [3,3,3]   0.001   [64,64,32] [2,2,1]    BBA Biomembranes (2023) 1865(6), 184174. doi: 10.1016/j.bbamem.2023.184174  
-ORF7b dimer 3 64 6 10 2500 0.05 [3,3,3]   0.001   [64,64,32] [2,2,1]    J. Phys Chem B. (2024) 128(1):150-162. doi: 10.1021/acs.jpcb.3c07105 +ORF7b dimer 3 64 6 10 2500 0.05 [3,3,3]   0.001   [64,64,32] [2,2,1]    J. Phys. Chem. B (2024) 128(1), 150-162. doi: 10.1021/acs.jpcb.3c07105 
-ORF7b dimer 3 64 6 8 2500 0.05 [3,3,3]   0.001   [64,64,32] [2,2,1]    J. Phys Chem B. (2024) 128(1):150-162. doi: 10.1021/acs.jpcb.3c07105 +ORF7b dimer 3 64 6 8 2500 0.05 [3,3,3]   0.001   [64,64,32] [2,2,1]    J. Phys. Chem. B (2024) 128(1), 150-162. doi: 10.1021/acs.jpcb.3c07105 
-BST-2/ORF7a 3 64 4 11 1000 0.05 [3,3,3]   0.001   [64,64,32] [2,2,1]    J. Phys. Chem. B (2026) 130 (5): 1553–1567. doi: 10.1021/acs.jpcb.5c07529+BST-2/ORF7a 3 64 4 11 1000 0.05 [3,3,3]   0.001   [64,64,32] [2,2,1]    J. Phys. Chem. B (2026) 130(5), 1553–1567. doi: 10.1021/acs.jpcb.5c07529
  
 </code> </code>
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 </code> </code>
  
-**Note: If the whole usage of data set is not a case, please specify the --start and --end  in the eval mode. **+**My suggestion is to adjust the number of input data points to an appropriate batch size to ensure 0 leftover.** 
 + 
 +**Note: The cluster label (in neither y tot.npy nor z tot.npy) would not be assigned to the leftovers. If the entire dataset is not used, please specify --start and --end in eval mode. **
  
 **1.4. Recommended Optimization Strategy** **1.4. Recommended Optimization Strategy**
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 </code> </code>
  
-The script below performs the following tasks:+The script performs the following tasks:
   * Reads one or more molecular dynamics trajectories; it has to follow exactly the data_collection setting.    * Reads one or more molecular dynamics trajectories; it has to follow exactly the data_collection setting. 
   * Loads GMVAE clustering results (y_tot.npy) from the specified cluster_folder.    * Loads GMVAE clustering results (y_tot.npy) from the specified cluster_folder. 
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   * Identifies the top representative conformations (highest cluster assignment probability) from each cluster.    * Identifies the top representative conformations (highest cluster assignment probability) from each cluster. 
   * Writes representative structures to individual trajectory files for downstream visualization and analysis.   * Writes representative structures to individual trajectory files for downstream visualization and analysis.
 +
 +**Example script**
 +
 <code> <code>
 #!/bin/bash #!/bin/bash
gmvae_update.1785688323.txt.gz · Last modified: 2026/08/02 12:32 by edit