VMD-L Mailing List

From: Raman Preet Singh (ramanpreetsingh_at_hotmail.com)
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.

Regards,
Raman