[gmx-users] second derivative of force

Nguyen Hoang Phuong phuong at theochem.uni-frankfurt.de
Wed Jun 21 09:01:25 CEST 2006


thanks Mark for the suggestion. I made an mistake in writing the first 
email. Actually, I need the first derivative of force, i.e, 
the second derivative of total energy.

Perhaps, a modification the code that computes the Hessian is a good idea. 
To do this, does anyone know exactly where is the code such that I just 
add the if command


...calculating the Hessian


Many thanks for your help.


> I don't think you'll find any short-cut, because I can't see that there is 
> another use for this type of calculation, hence nobody will have included it 
> already in GROMACS. Hessian matrices are expensive to calculate for QM 
> because they scale with something like the fourth power of the number of 
> basis vectors. The cost of finding Hessian matrices in MM is roughly linear 
> in the number of atoms, so it ought not to be too scary. In fact, it would 
> only be more expensive by a factor of N over an algorithm that only 
> calculates the diagonal terms. If it is too expensive, you also might want to 
> reconsider doing it at every trajectory snapshot :-) Otherwise, your only 
> recourse will be to find the piece of code that computes the Hessian, and 
> rework the loops over i and j so that i=j always.
> Mark
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