Currently I use Gromacs to perform molecular dynamics of tobermorite 11A, but it turns out that this structure has a monoclinic box, I need to solvate my structure only above in the z axis, but I have problems, because gromacs does not allow to solvate with angles, so some molecules of solvent are located outside the box .... how could I do this?
Everth Vargas If you want to add water molecules to a specific section of your box without using gmx solvate, you may be able to use the gmx insert-molecules command. You'll essentially need a PDB/GRO file of your desolvated tobermorite 11A, a PDB of a single water molecule, and a positions.dat file. The positions.dat file will have a line for every water molecule you intend to add.
I have a longer explanation about how to use the gmx insert-molecules command with much more detail below. This was advice I gave for a membrane system, but the principles still apply.
https://www.researchgate.net/post/How_to_setup_double_bilayer_system_in_Gromacs
Hi Everth!
I do not know which version of gromacs you are using but I always install several verions on my computer and, particularly, 4.6.7. It has different options for the insertion of water molecules and in my opinion, genbox works better than many new routines. You can create a gro/pdb file using the old version then you can source the new version and run the simulation. I can add that the old verion can simply put SPC water in your box, then you might need to rename atoms for the desired water-model which you plan to use for your simulation.
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