I have protein-membrane simulations (PDB, PSF, DCD) and have noticed that water molecules near the protein are not visible in the simulations. How can I fix this issue? Is there a way to place the missing water molecules and save the updated PDB, PSF, and DCD files without having to rerun the simulation from scratch? Are there any methods to fill the uncovered protein areas with water molecules?
I have been using NAMD tool. I would be more than happy if you could suggest me and I am looking forward to hearing from you all.
#NAMD #VMD #water #trajectory #DCD #protein #membrane #CHARMMGUI
As you allude to in your question, the waters most likely do exist but are just not "showing" the way you want them to. This is probably happening because of the periodic boundary treatment you are imposing on the structure which seems to make all molecules whole. As water molecules are small, you don't notice how the treatment affects water molecules. But since the protein is large and stretches across the Z-dimension's periodic boundary, the end of it is shown in what appears to be vacuum, but this is a visual artifact as the protein is actually surrounded by the waters at the top of your image.
If you want to just get it visualized properly, you can follow these instructions:
1) Open VMD
2) Select Graphics > Representations
--> this will open the Graphic Representations window
3) Click "Create Rep"
4) Type water into "selected atoms"
5) Click "Apply"
6) Click the "water" representation
7) Select Periodic tab
8) Check the +Z and -Z boxes
Follow the same procedure for "Protein." This should create additional periodic images of the water protein, showing your system as it actually is simulated.
Jd Tamucci thank you so much. I really appreciate your suggestions. I had actually tried that approach before, but I was looking to save the new PDB and DCD files after making a selection through the Periodic tab (checking +Z and -Z). There are commands like pbc get, pbc set, and pbc wrap that help to display water molecules that were not visible before due to PBC issues. I'd be happy to help anyone facing similar issues. Feel free to reach out to me.
Thanks again, Jd Tamucci
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