[gmx-users] (no subject)

[Nguyen Hoang Phuong]

> Nguyen Hoang Phuong wrote:
> 
> > As I understood, the array elements x[i][j] computed by the nmrun and
> > stored in the hessian.mtx are not really the matrix element of the
> > Hessian, but they should be -x[i][j]. If this is the case, then my results
> > are as same as those computed by g_nmeig. I'm wondering about this and
> > can anyone correct me? Thanks in advance.
> > 
> 
> I guess that's exactly why g_nmeig reads -x instead of x. I don't remember
> the deeper meaning for this (if any) so I'd assume your code is OK.
> 
> Bert
> 

Dear Bert,

The Hessian : H_{ij}=\frac{\partial^2 V}{\partial x_i \partial x_j}

The force: F= - \frac{\partial V}{\partial x_i}

In GROMACS, the H_{ij} is computed numerically from force, i.e,

 H_{ij}= - \frac{\partial F}{\partial x_i}

I guess the program nmrun calculates the quantities \frac{\partial
F}{\partial x_i} and therefore the g_nmeig must add - to the  H_{ij}.

Regards,

Phuong

> ____________________________________________________________________________
> Dr. Bert de Groot
> 
> Max Planck Institute for Biophysical Chemistry
> Theoretical molecular biophysics group
> Am Fassberg 11 
> 37077 Goettingen, Germany
> 
> tel: +49-551-2011306, fax: +49-551-2011089
> 
> email: bgroot at gwdg.de
> http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
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