On 14/06/2012 6:10 PM, Hyuntae Na wrote:
> Message: 1
> Date: Thu, 14 Jun 2012 17:19:51 +1000
> From: Mark Abraham <[email protected]>
> Subject: Re: [gmx-users] (3x3) Hessian matrix without minimization
> To: Discussion list for GROMACS users <[email protected]>
> Message-ID: <[email protected]>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On 14/06/2012 5:04 PM, Hyuntae Na wrote:
> > Dear All,
> >
> > I want to get a hessian matrix without minimizing a protein molecule.
> > Essentially, I want to get the 3x3 hessian matrice of each atom
(which
> > is the diagonal term of the 3n x 3n hessian matrix). Would you
help me
> > to get it?
>
> Check out manual section 7.4 for hints on which tools are useful for
you
> - then appendix D for more details.
>
I had done the NMA (Normal Mode Analysis) with sequentially calling
pdb2gmx, grompp, mdrun, grompp_d, mdrun_d, and gmxdump_d in order to
minimize the protein structure with L-BFGS (with the final
minimization step with mdrun_d), and in order to get the hessian
matrix with text format.
I especially want to get the *hessian matrix with a non-minimized
protein conformation*.
Doesn't choosing integrator = nm in your .mdp just do that?
Mark
--
gmx-users mailing list [email protected]
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 [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
