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.abra...@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 > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com
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