Dear community,
I am doing a slab geometry of upper and lower Silicon wall with KCl solution in between. (K+: POT, Cl-: CLA)
The interaction between potassium-water (POT-OW) and chloride-water (CLA-OW) is important to my simulation.
Therefore, combine the LJ parameters of POT-OW and CLA-OW to the [ pairtypes ] ffnonbonded.itp in charmm36.ff.
[ atomtypes ]
;type atnum mass charge ptype sigma epsilon
SI 14 28.085500 0.000 A 0.3386 2.447 ; Gromacs manual 3.0
POT 19 39.098300 0.000 A 0.3335 0.418371 ;"Atomistic simulation" use
CLA 17 35.450000 0.000 A 0.4405 0.418371 ;"Atomistic simulation" use
HW 1 1.008000 0.41 A 0.0 0.0
OW 8 15.999400 -0.8476 A 3.165e-01 6.503e-01 ; Gromacs manual 3.0
[ pairtypes ]
; i j func sigma epsilon
OW CLA 1 0.3785 0.5216 ; Koneshan et al. 1998
OW POT 1 0.325 0.5216 ; Koneshan et al. 1998
OW SI 1 0.32755 1.261461 ; Calculated from SI-SI in Gromacs manual 3.0
However, there is no POT-OW and CLA-OW defined in the [pairs] of my topology file.
I would like to know
- whether the LJ parameters defined in ffnonbonded.itp is actually been used during the simulation?
- Do I need to define the POT-OW and CLA-OW to let Gromacs to calculate the interaction force between them? or Gromacs will automatically calculate it because I set gen-pairs = yes in the [default] of the forcefield.itp?
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 1.0 1.0
- Does the ions.itp have any effect on it?
[ moleculetype ]
; molname nrexcl
K 1
[ atoms ]
; id at type res nr residu name at name cg nr charge
1 POT 1 K K 1 1
Thank you for reading my questions.
Any comment is highly appreciated.