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> Message: 1<br>> Date: Thu, 14 Jun 2012 17:19:51 +1000<br>> From: Mark Abraham <Mark.Abraham@anu.edu.au><br>> Subject: Re: [gmx-users] (3x3) Hessian matrix without minimization<br>> To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>> Message-ID: <4FD99097.90803@anu.edu.au><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> <BR>Thanks.<BR> <BR>Best regards,<BR>-- Hyuntae<BR><br>> Mark<br>> -------------- next part --------------<br>> An HTML attachment was scrubbed...<br>> URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20120614/6dcbb483/attachment-0001.html<br><BR> </div></body>
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