From: Raman Preet Singh (
Date: Sat Aug 28 2021 - 08:43:43 CDT

Dear VMD users,

I am interested in simulating a system with phosphate (PO43-) ions and Na+ (or K+) counterions. VMD autoionize plugin does not contain this species. Is there a way to add sodium phosphate (or potassium phosphate)

  1. At a specific concentration (say, 1 mM)
  2. A specific number of molecules in simulation box (say, 100 per box of fixed dimensions)

One way is to manually replace TIP3P water molecules in the pdb and psf but I would like to avoid that since there are several system configurations that need to be tested and simulated. Any VMD hacks or script to do this will be highly appreciated.