GROMACS version:2020
GROMACS modification: Yes/No
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Can I ask the relation between “-water spce” (gmx pdb2gmx) and “-cs spc216.gro” (gmx solvate). My understanding is, they both specify the type of water molecules. But why we need to do these separately?
Justin’s tutorial said “You can use spc216.gro as the solvent configuration for SPC, SPC/E, or TIP3P water, since they are all three-point water models.” So why a same .gro file can be used for different water models? What does spc216.gro actually mean?
the “-water spce” in pdb2gmx is optional, please use spc216.gro for all three-points water models, tip4p.gro for four-points water models
and tip5p for five-points water models
spc216.gro is a pre-equilibrated box of 216 SPC water molecules. It can be used as the source of water coordinates for any 3-point water model because they all only vary slightly. After minimization and equilibration using the desired water force field, you’ll recover the proper behavior of TIP3P, SPC/E, etc.
The topology is called spc.itp. There is no linkage to the number of water molecules in the pre-equilibrated coordinates (216).
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