[gmx-users] Hessian Matrix Doubt

Berk Hess gmx3 at hotmail.com
Fri Aug 3 16:56:30 CEST 2007

>From: Anirban Ghosh <anirbanz83 at yahoo.co.in>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: GROMACS <gmx-users at gromacs.org>
>Subject: [gmx-users] Hessian Matrix Doubt
>Date: Fri, 3 Aug 2007 06:55:34 +0100 (BST)
>Hi All,
>I want to go for Normal Mode Analysis of a protein in water. I have done 
>the energy minimization of the protein with water molecules. But now I want 
>to calculate the Hessian Matrix with only the protein molecules and not the 
>water molecules. Please tell me how to do that. Is there any option in 
>Please suggest.

This requires some linear algebra, which is unfortunately not (yet) 
implemented in Gromacs,
see the following mail for the formula:


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