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Hi, all
I am trying to select the polarizable water model for my simulation. Where to get the tip4p-fq.itp?
By the way, swm4-ndp.itp found in http://mackerell.umaryland.edu/charmm_drude_ff.shtml, but the gmx genion seemed could not add ions correctly.
Many thanks
I may be wrong since I haven’t use polarizable water model.
I think one way is to use the TIP4P model since both are 4 site water models.
I am afraid you may need to manually update the force field of water model in the topology file if your gromacs doesn’t have the corresponding water potentials.
Lastly, run a quick energy minimization, which should eliminate the differences in the water structures.
It does if you check out the Drude branch of the GROMACS git repository, but it’s still being worked on. gmx genion will work and will add polarizable ions to the system automatically.
gmx genion could only add one atom ions，but ions has two atom in ions.itp of Drude. If I manually add the second atom of ions, after gmx grompp, gmx could not find the default bond type
I’m not sure what do you mean, I need change the parameters in tip4p.itp?
gmx genion can update the toplogy file *.top if you selected this option.
I don’t think GROMACS includes tip4p-fq potential by default.
Therefore, you need to edit *.top the one that will be compiled into the *.tpr file for mdrun.
The error messages indicates some inconsistency in your *.top file (and the associated itp files).
It seems that new atom types are introduced but the corresponding bonds are not properly defined.
