[gmx-users] NMA for a group

Lars Schaefer Lars.Schaefer at mpi-bpc.mpg.de
Mon Jun 25 23:08:48 CEST 2007

Christian Seifert wrote:
> On Friday 22 June 2007 11:22, Lars Schaefer wrote:
>>Hi Christian,
>>I am not sure what exactly you need the Hessian for. But if you are
>>interested in IR spectra, you might also calculate them from dipole
>>autocorrelation (instead of from the hessian).
> You are right. We are interested in IR spectra calculated by GMX/CPMD. We have 
> already done this with EGO/CPMD. Obviously it is not possible to calculate a 
> hessian of a subsystem with gromacs. 

A complete QM/MM Hessian contains, apart from the rather straightforward
QM/QM and MM/MM parts also the mixed blocks (see e.g. paper below). So:
No, QM/MM second derivatives is not implemented in GROMACS (yet).

author={Q.~ Cui and M.~ Karplus},
title={Molecular properties from combined QM/MM methods. I. Analytical
second derivative and vibrational calculations},
journal={J. Chem. Phys.},
number={3} ,

Thus we have to calculate the IR spectra
> from dipole autocorrelation.
> Thanks to all of you for your help
> Christian.
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