Hello, I would like to ask why after adding water solvent, the middle will appear in some places blank. Why aren’t these water molecules here?And what can I do to replace these missing water molecules? Or is there any code that just fills the bottom half of the box with water? Thank you
Please provide the exact sequence of commands you have given. What you’re showing is very unusual.
the code is “gmx solvate -cp em-vac.gro -cs spc216.gro -p fws.top -o fws-b4ion.gro -box 4 4 2” em-vac.gro is the ozone molecule .
It seems to me that the ozone coordinates are not centered in the specified box, so they are, in fact, there but they appear to be “outside” the box. If rewrapped, you are probably getting the ozone/water layer that you expect. Normally one centers a solute within a given unit cell and then adds solvent after the fact.
But I added the water solution after I created the box with the code“ gmx editconf -f fws.gro -o fws-PBC.gro -bt cubic -box 4 4 4 ” and put the ozone molecule in the center.
And then you are telling gmx solvate to use a different box with -box 4 4 2. If you want to create a layered system, there is an approach discussed here: Building Biphasic Systems
In fact, I just want to fill the bottom half of the box with water molecules with ozone, is that creating a layered system? If not, then what should I do.
I don’t understand your question. Can you diagram out what you’re trying to accomplish?
I wanted to implement this model
Then the approach is the same as in the tutorial. Build the initial box of ozone, position it in a new box that is doubled in size along one axis, and solvate the void space with water. If that leads to water being mixed with the ozone layer, then simply generate two boxes with the appropriate dimensions and concatenate them.
Excuse me, I would like to ask how to connect the two boxes together. And I want to know if the initial ozone box was not completely filled with ozone molecules，at this point,whether making the box extended, and then using water solvent will cause the entire large box to be filled with water or not.