[gmx-users] Hessian Matrix Doubt

Mark Abraham Mark.Abraham at anu.edu.au
Fri Aug 3 08:08:26 CEST 2007

Anirban Ghosh wrote:
> 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 GROMACS?

You may want to use double precision minimization, then use trjconv on 
your output .trr file to do what you want to do. Read the man page for 


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