> Message: 1 > Date: Thu, 14 Jun 2012 17:19:51 +1000 > From: Mark Abraham <mark.abra...@anu.edu.au> > Subject: Re: [gmx-users] (3x3) Hessian matrix without minimization > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4fd99097.90...@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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20120614/6dcbb483/attachment-0001.html
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