Nguyen Hoang Phuong wrote:
Dear All,
I would like to obtain the second derivative of the total force
d^2f_i/dr_i^2 at every atom i along the trajectory. In principle, this
can be
obtained from the Hessian matrix. However, I don't need the cross terms
like d^2f_i/dr_i dr_j, therefore it will be very time consumming to
calculate
the Hessian matrix along the trajectory if I just need the off-diagonal
terms. Does anyone know a way to do that? Thanks.
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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