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gmvae_update

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gmvae_update [2026/08/02 06:49] – editgmvae_update [2026/08/03 12:43] (current) – edit
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 This is based off Dr. Ghorbani's GMVAE code available on [[https://github.com/ghorbanimahdi73/GMVAE-MD|Github]]. This has been updated to work with newer versions of python and Zaratan's architecture. Use on other HPC will likely need tweaking from the instructions below. This is based off Dr. Ghorbani's GMVAE code available on [[https://github.com/ghorbanimahdi73/GMVAE-MD|Github]]. This has been updated to work with newer versions of python and Zaratan's architecture. Use on other HPC will likely need tweaking from the instructions below.
  
-Tar file for all code: {{ :gmcave_tf1_update_copy.tgz |}}+Tar file for all code:  {{ :gmvae_tf1_v2.tgz |}}
  
 The detailed instructions were added by Dr. Min-Kang Hsieh. The detailed instructions were added by Dr. Min-Kang Hsieh.
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 </code> </code>
  
-**Usage note: copy the scripts folder as your project name to begin.**  +**Usage note: copy the scripts folder as your project name to begin.** 
 +  
 +Note: If the servers where no graphical user interface (GUI) or display server is available,  add matplotlib.use("Agg") before importing pyplot to force Matplotlib to use a non-GUI backend, allowing you to generate and save plots without opening a visual window.  
 + 
 +<code> 
 +import matplotlib 
 +matplotlib.use("Agg")  
 +import matplotlib.pyplot as plt 
 +</code> 
 + 
 + 
  
 **Input data preparation** **Input data preparation**
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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.1785667799.txt.gz · Last modified: 2026/08/02 06:49 by edit