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
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