[gmx-users] (no subject)
Nguyen Hoang Phuong
phuong at theochem.uni-frankfurt.de
Thu Jul 18 14:47:48 CEST 2002
> 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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