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

Hyuntae Na htna at hotmail.com
Thu Jun 14 10:10:56 CEST 2012

> 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*. Thanks. Best regards,-- Hyuntae
> Mark
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