[gmx-users] Re: Dihedral Constraints

bharat gupta bharat.85.monu at gmail.com
Thu Jun 14 08:38:48 CEST 2012

Thanks Sir for the reply... This question is related to my first query that
if we constraint the dihedral of the turn residue how can we fix/freeze the
movement of other residues. As I am interested in only getting the energy
of the hairpin when the turn residues are constrained within a particular
phi psi angle range....

On Thu, Jun 14, 2012 at 11:21 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> 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
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