[gmx-users] TIP4P, TIP4P-Ew
chihying2008 at gmail.com
Sun Sep 28 06:16:46 CEST 2008
I followed the tutorials
the procedure is
1. create the box
Use a standard cubic box and be sure that the protein does not see its
images. This means that the distance from the the box wall should be greater
than half of the cut-off (1.4 nm)
editconf -f minimized.gro -o minimized_box.gro -d 0.75 -bt cubic
2. solvate the protein
genbox needs as input the protein in a box (minimized_box.gro) and a solvent
box (spc216.gro) and the topology of the solute (aki.top) and of the solvent
genbox -cp minimized_box.gro -cs spc216.gro -o minimized_water.gro -p
Is it the same thing for the TIP4P-Ew water model?
> Then, I can say my system is under the water model-TIP4P-Ew.
> And, other simulation procedures are all the same for any kind of water
What procedures do you mean?
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