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On 14/06/2012 6:10 PM, Hyuntae Na wrote:
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> Message: 1<br>
> Date: Thu, 14 Jun 2012 17:19:51 +1000<br>
> From: Mark Abraham <a class="moz-txt-link-rfc2396E" href="mailto:Mark.Abraham@anu.edu.au"><Mark.Abraham@anu.edu.au></a><br>
> Subject: Re: [gmx-users] (3x3) Hessian matrix without
minimization<br>
> To: Discussion list for GROMACS users
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a><br>
> Message-ID: <a class="moz-txt-link-rfc2396E" href="mailto:4FD99097.90803@anu.edu.au"><4FD99097.90803@anu.edu.au></a><br>
> Content-Type: text/plain; charset="iso-8859-1"<br>
> <br>
> On 14/06/2012 5:04 PM, Hyuntae Na wrote:<br>
> > Dear All,<br>
> ><br>
> > I want to get a hessian matrix without minimizing a
protein molecule. <br>
> > Essentially, I want to get the 3x3 hessian matrice of
each atom (which <br>
> > is the diagonal term of the 3n x 3n hessian matrix).
Would you help me <br>
> > to get it?<br>
> <br>
> Check out manual section 7.4 for hints on which tools are
useful for you <br>
> - then appendix D for more details.<br>
> <br>
<br>
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.<br>
<br>
I especially want to get the *hessian matrix with a
non-minimized protein conformation*. <br>
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<br>
Doesn't choosing integrator = nm in your .mdp just do that?<br>
<br>
Mark<br>
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