[gmx-users] Re: Dihedral Constraints

[Mark Abraham]

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.

http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints

> 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?

Mark

>
>
> 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.
>
>     Mark
>
>     -- 
>     gmx-users mailing list gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at
>     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-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read 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 : monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>
>
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120614/78a69012/attachment.html>