[gmx-users] Re: Dihedral Constraints
Mark.Abraham at anu.edu.au
Thu Jun 14 08:50:59 CEST 2012
On 14/06/2012 4:38 PM, bharat gupta wrote:
> 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....
.. and with what are you going to compare those energies? And what will
that comparison mean?
> On Thu, Jun 14, 2012 at 11:21 AM, Mark Abraham
> <Mark.Abraham at anu.edu.au <mailto: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.
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