[gmx-users] (3x3) Hessian matrix without minimization

[Mark Abraham]

On 14/06/2012 6:10 PM, Hyuntae Na wrote:
> > Message: 1
> > Date: Thu, 14 Jun 2012 17:19:51 +1000
> > From: Mark Abraham <Mark.Abraham at anu.edu.au>
> > Subject: Re: [gmx-users] (3x3) Hessian matrix without minimization
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <4FD99097.90803 at anu.edu.au>
> > 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
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