In nbonds.doc, their definitions are:
CDIE - Constant dielectric. Energy is proportional to 1/R.
RDIE - Distance dielectric. Energy is proportional to 1/(R-squared)
And they are used in the following minimization examples:
1) minimize sd nstep 50 cdie eps 1.0 fshift vshift cutnb 13.0 ctofnb 12.0 !Copy from professor Lennart Nilsson's minimize.inp(scripts forum)
2) minimize conj nstep 500 tolenr 0.001 cutnb 14.0 rdie eps 2.0 vswitch shift
My questions are:
a. If I use "RDIE", then what is the dielectric constant of all the selected atoms? What does the "distance dielectric" explicitly mean? Any formula?
b. If I want to minimize a protein in solvent(water), what should I use? And How?
Thank you very much!