[gmx-users] Re: Dihedral Constraints

[Mark Abraham]

On 14/06/2012 12:04 PM, bharat gupta wrote:
> Thanks for the reply . Is it possible to calculate the dihedral energy 
> of certain residues, like in my case for turn residues ??.. How can 
> that be done

First, seek to define "dihedral energy"... Force fields are not 
parametrized such that parts of them are expected to correlate with 
observables.

>
> This another question is regarding energy minimization. Suppose, I 
> minimize the the protein solvated in water, the energy value that I 
> get is for the whole system or for the protein alone. If it's for the 
> system then how can I get the energy for the protein alone.

You can define energy groups (see manual) to do this for the nonbonded 
contributions. Bonded contributions are easy to do in your case. Whether 
this energy is useful for anything is quite another matter.

Mark