David A. Case wrote:
>On Tue, Jan 21, 2003, Seongeun Yang wrote:
>
>
>>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.
>>
>>
>
>
>
>>But in all cases, two ions get together while equilibrating the box and
>>energy explodes.
>>
>>
>
>We would need more details; this should not be happening. You might
>try turning off vrand, but I suspect there is something funny about your
>system that is not obvious from the information you gave.
>
>..regards...dac
>
>
Thanks for your comments.
I tried again for the case with the following sets of commands in amber.
I used parameters of Na+ and Cl-(type IM) in parm99.dat.
The input file for the equilibration at 10K looks like this.
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 = 1, nscm = 100,
nstlim = 5000, dt = 0.002,
ntt = 1, vrand = 100,
lastist = 10000000, lastrst = 10000000,
The box is heated from 10K to 300K using vrand = 100, and then vrand is
off to 0 in NPT condition.
After preparing library file for Na+(unit1) alone and loading it,
1. solvatebox unit1 WATBOX216 9.0
addions unit1 Cl- 0
-- Then, initially Cl- is added just beside Na+ and energy blows out
aroundNSTEP=200.
2. solvatebox uni1 WATBOX216 9.0
addions unit1 Na+ 1
savepdb unit1 pdb (edit Na+ to Cl- in pdb file and reload the new pdb)
unit2=loadpdb newpdb
edit unit2 (edit parameters of Na+ and Cl-)
setbox unit2 vdw
-- Then, energy blows out around NSTEP=50.
3. the same as 1 except for using 10.0 for setting the box size
-- Then, energy blows out around NSTP=150.
4. the same as 2 except for using 10.0 for setting the box size
-- Then, energy blows out around NSTEP=700.
All these are occurred during equilibrating the box at 10K with NVT
condition.
But for much larger boxes, this problem doesn't occur.
Seongeun
Received on Fri Jan 24 2003 - 16:13:41 PST
