Klauda Lab Simulation Wiki

User Tools

Site Tools

Trace: • gmvae_update
Writing /users/jbklauda/pub/wiki/data/cache/3/36a3922e6748748aba38e43b093b0858.i failed
Unable to save cache file. Hint: disk full; file permissions; safe_mode setting.
Writing /users/jbklauda/pub/wiki/data/cache/3/36a3922e6748748aba38e43b093b0858.metadata failed
Writing /users/jbklauda/pub/wiki/data/cache/6/6193a558dc90ed4c190004bf67ecff70.captchaip failed
gmvae_update

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision		Previous revision
gmvae_update [2026/08/02 21:03] – editgmvae_update [2026/08/03 12:43] (current) – edit
Line 361: Line 361:
 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>
Line 398: Line 398:
 </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**
gmvae_update.1785719013.txt.gz · Last modified: 2026/08/02 21:03 by edit