[gmx-users] Hessian matrix conversion

[Erik Lindahl]

Hi,

On May 15, 2006, at 10:02 PM, Lei Zhou wrote:

> Hi,
>
> I am trying to convert the binary Hessian matrix (nm.mtx) into a  
> readable ascii format. According to the recommendations on this  
> email list, I rename the nm.mtx to nm.trr and tried to use gmxdump.  
> However, there is an error message liketrn version:
>
> Program gmxdump, VERSION 3.3.1
> Source code file: trnio.c, line: 69
> Fatal error:
> Float size 401. Maybe different CPU?
>
> I am using gromacs 3.3.1. Also I am wondering there is any new  
> update on the extration of C-alpha modes based on the all-atom  
> Hessian matrix? Thanks for the help.

We had to discard the old Hessian format when introducing the sparse  
matrix representation to enable NMA for huge molecules. The easiest  
way to extract the data is probably to have a look in src/tools/ 
gmx_nmeig.c.

As for C-alpha modes, projections of orthogonal vectors onto a  
subspace won't be orthogonal in that subspace, so per definition they  
are not "normal" modes for C-alpha. If you really want Ca-only modes  
you are probably better of with an elastic network model online  
server, e.g. http://lorentz.immstr.pasteur.fr .

Cheers,

Erik