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
Received on Tue Jan 21 2003 - 14:48:04 PST
