[gmx-users] How to add solvent in a Biphasic Systems ?

[Jinfeng Huang]

Dear gromacs users,


    I want to build a liquid-solid system following the tutorial "Building Biphasic Systems" (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/index.html ), but I have met two problems during my operation.


    1) After adding a protein to the liquid layer, the tutorial describe as "Then proceed with another round of solvate to add water, as before." I don't know how to add the water. I used the "solvate" command and there will be a lot of waters added in the solid layer (There are no waters added in the solid layer after I changed the value of the C radius when I solvate the solid layer only). How should I solvate the protein-solid system without waters added in the solid layer?


    2)How to add TIP3P water models with the solvate command in gromacs instead of the spc216 water model?
   It's highly appreciated if there are any suggestions.
Jingfeng