AMBER Archive (2003)

Subject: problems in equilibrating NaCl solution

From: Seongeun Yang (seongeun_at_ccb.wustl.edu)
Date: Tue Jan 21 2003 - 16:48:04 CST

Hi all,

I'd like to get the free energy change for Na+ -> K+ perturbation in water.
To do this, I've been trying to prepare equilibrated NaCl solution.
For one pair of Na+ and Cl-, the smallest box I used is from
   solvatebox unit WATBOX216 9.0
The unit is a Na+, and Cl- is added after solvation using
   addions unit Cl- 0
or
   addions2 unit Cl- 0
or
   addions unit Na+ 1
then replacing Na+ with Cl- and correcting the topology file with a few
commands.
I tried also to replace one water molecule, randomly chosen in unit
editor, with Cl-.
But in all cases, two ions get together while equilibrating the box and
energy explodes.
I tried also with larger water boxes, but if I'd like to use the
concentration of NaCl used
in 'solvatebox unit WATBOX216 9.0', what is a reasonble way to do this ?

The NaCl solution is heated starting from 10 K to 300K using NVT condition
and then equilibrated using NPT condition at 300K.
One of the input files I used looks like:
   imin = 0,
   ntx =1, irest = 0,
   tempi = 10.0, temp0 = 10.0,
   ntwe = 50, ntwr = -5000,
   ntf = 2, ntb = 1, ntc = 2,
   cut = 10.0, nsnb = 10, nscm = 100,
   nstlim = 5000, dt = 0.002,
   ntt = 1, vrand = 100,
I tried also smaller values for nscm and vrand if the equilibration failed.

Waiting for some good ideas for this...

Seongeun Yang