Talk:Mod:Hunt Research Group/ChemShell Force Field Parameters Aqueous Cu(II)

Creating a File Containing Force Field Parameters

The following ChemShell code generates a file called ff.dat which contains force field parameters for our copper-water system:

read_input ff.dat {
vdw cu cu  62.99111 19858.39
vdw cu  o  204.1966 118331.2
vdw cu  h  0.000000 0.000000
vdw  o  o    626.00 630437.34
vdw  o  h    0.0000 0.000
vdw  h  h    0.0000 0.000
bond o  h   1108.57 1.000
charge  o   -0.8476
charge  h    0.4238
charge cu    2.0000
angle h o h 91.5392 109.4
}

To run, login to cx1, put the code into a file (call it ff.chm). Make sure the ChemShell module is loaded (module load chemshell/3.5.0), and then execute:

chemsh.x ff.chm

If successful, you should see ff.dat created with the following contents:

vdw cu cu  62.99111 19858.39
vdw cu  o  204.1966 118331.2
vdw cu  h  0.000000 0.000000
vdw  o o 626.00  630437.34
vdw  o h 0.0000  0.000
vdw  h h 0.0000  0.000
bond o h 1108.57 1.000
charge o  -0.8476
charge h   0.4238
charge cu  2.0000
angle h o h 91.5392 109.4

ff.dat can be directly used as input into our copper-water ChemShell calculations which involve a force field.

The vdw keyword specifies pairwise non-bonded Lennard-Jones interactions.

The bond keyword specifies harmonic bond parameters between two atoms.

The charge keyword sets the electrostatic charge on an atom.

The angle keyword specifies harmonic angular terms between 3 atoms.

More details on these terms and other terms can be found here.

NB: Be careful when transferring parameters from a different program into ChemShell as they may be defined differently and/or have different units! See the table below for an example.

Program	Keyword	Potential Form	Param. 1 (default units)	Param. 2 (default units)
ChemShell	`vdw`	$U (r_{i j}) = - \frac{C_{6}}{r_{i j}^{6}} + \frac{C_{12}}{r_{i j}^{12}}$	$C_{6}$ (kcal mol $- 1$ Å $6$ )	$C_{12}$ (kcal mol $- 1$ Å $12$ )
DL_POLY	`lj`	$U (r_{i j}) = 4 ϵ [{(\frac{σ}{r_{i j}})}^{12} - {(\frac{σ}{r_{i j}})}^{6}]$	$ϵ$ (J mol $- 1$ )	$σ$ (Å)