Relation between "-water spce" and "-cs spc216.gro"

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1

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?

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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

3

Thanks, but there must be some meaning of using “-water spce”, or “-water spc”, or “-water tip3p”, what is the meaning?

4

You specify the type of water model that is routed to the end of the topology file for related force field, for example, if you use -water tip3p,

in end of topology you can find:
; Include water topology
#include “…ff/tip3p.itp”

5

Yes, “…ff/tip3p.itp” will use the tip3p water model, “…ff/spce.itp” will use the SPC/E water model. But are they both using the spc216.gro?

Why not just writting it as, e.g. “…ff/spc216.itp”?

6

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).

7

Thank you Justin, that is much clearer now. I did not know “216” means 216 water molecules.

9

Your question is not closely related to the original thread, which has been inactive for almost three years. Please start a new thread (with a descriptive title) with your question. That will make it easier for others to find it, both to help you now and for others with the same problem later.

10

thanks for replying.