AIMD/MM


  • Guest -
10:35:55 AM PDT - Sun, Jul 17th 2011
Hi All,

I am trying to use the AIMD/MM method in the NWPW module. Acoording to the documentation, quadratic bond-stretching and bond-bending parameters for the MM region can be specified using directive "bond_spring" and "angle_spring" respectively. I am wondering whether it is also possible to specify Morse bond-stretching and dihedral parameters?

Furthermore, is it possible to add link atoms in AIMD/MM simulations?

Peizhi

Gets Around
3:53:01 PM PDT - Wed, Aug 17th 2011
Peizhi,

The documentation is a little out of date.
The following keywords are available in the fragment blocks of AIMD/MM
> 'size',
> 'index_start',
> 'shake',
> 'switching',
> 'bond_spring',
> 'angle_spring',
> 'self_interaction',
> 'incell',
> 'cross_bond_spring',
> 'bond_morse',
> 'dihedral_spring',
> 'dihedral',
> 'coord_number',

The input (in au) for bond_morse, dihedral, and dihedral_spring are as follows

bond_morse i1 i2 k a re
where
E = E + k*( 1.0d0 - dexp(-a*(r-re))) )**2
and
r is the distance between atoms i1 and i2


dihedral_spring i1 i2 i3 i4 k theta0
where
E = E + k*(phi-theta0)**2
and
phi is the torsion angle spanned by atoms i1 i2 i3 and i4


dihedral i1 i2 i3 i4 k a0 theta0
where
E = E + k*(1.0+cos(a0*phi-phi0))

I still haven't implemented link atoms but will probably do so in the near future.

Hope that helps
Eric


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