From: 김민재 (
Date: Tue Feb 19 2019 - 19:51:03 CST

Hi everyone.

I am currently trying to run a MD simulation with TIP4P water. I am
relatively new to this. So, I followed the namd tutorial to solvate
carbonic anhydrase in a water box (5 angstroms longer than the atoms with
the highest coordinates in the x,y, and z axes.) However, in the resulting
pdb file, I noticed that the water was TIP3. Would it still be okay to run
the simulation with the configuration set to "waterModel tip4"? If not, how
can I create a waterbox with TIP4 water?

I tried using vmd’s solvent builder. However, I am confused as to how I
should supply the solvate process with a pdb and psf file (when I check
“use other solvent,” vmd requires me to refer to pdb, psf, and topology
files) when I haven’t built my tip4_water.pdb yet. Also, once the build and
equilibriate my water box, how can I solvate my protein within the water

I would really appreciate help on this issue.