... as far as I know, the ions are placed
very close to the solute (within 5 Angstrom of solute atoms) in this
procedure.
Yes, this is done for speed.
I am not sure this is the best way to model an ionic solution.
It seems to be introducing a bias.
Definitely so.
Wouldn't it be better if ions were placed totally randomly in the space
around the solute?
This might lead to a better equilibrated system, especially in the case
of solvated protein systems.
For the time being, the simple solution is to equilibrate using
constant volume and belly (only water and ions moving) to allow
the ions to become distributed. No gradual warming is necessary
(assuming md starts ok), and high temperature can be used. Then
minimize briefly or throw away velocities & start warming the
whole system gradually.
Bill Ross
Received on Mon Feb 12 2001 - 14:52:07 PST
