A molecular-dynamics study of the rhodopsin chromophore using ultrasoft pseudopotentials

We investigate the effect of different environments on the chromophore of t he protein rhodopsin by using the Vienna ab initio simulation package which is based on Density Functional Theory with a plane wave basis set and the implementation of Vanderbilt's ultrasoft pseudopotentials, We have calculat ed the energy dependence of Il-cis-retinal on the C11-C12 double bond twist angle in the ground state and our results show that the isomerization in t he ground state of the retinal chromophore is more difficult in the presenc e of the counter ion than without it.