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I am trying to fully populate my GROMACS simulation, but the water density in the bulk is too low.

Here are the steps I used:

  1. Add organic monolayer into 9x9x9 box

  2. Solvate with water

  3. equilibrate t-coupled, then p,t coupled

  4. expand box to 9x9x30 (to create interface, this allows for organic molecules to form a monolayer)

  5. equlibrate t-coupled

  6. prod

The problem seems to be with step 2 as GROMACS can only seem to fit 0.9 g/ml of water in the original system (because there are a bunch of organic molecules), is there a way to force it to have a certain density?

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    $\begingroup$ Shouldn't gmx insert-molecules resolve your problem? $\endgroup$ Nov 30, 2023 at 10:06
  • $\begingroup$ you mean to add more water molecules? Since I already use it for the organics $\endgroup$
    – Peter Yang
    Nov 30, 2023 at 19:12
  • $\begingroup$ Yes, you can do that. Add more water molecules. $\endgroup$ Nov 30, 2023 at 19:58
  • $\begingroup$ You can do the same for water molecules as well. Try to add the water molecules to get the density you want. $\endgroup$ Dec 1, 2023 at 10:43

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Solvation in gromacs is not limited to only with gmx solvate. As I discussed with you in the comments section, we can have an estimate on the number of water molecules you need to add to get the right density you want, and then use gmx insert-molecules to add the right number of water molecules.

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