[gmx-users] NMA for a group

David van der Spoel spoel at xray.bmc.uu.se
Mon Jun 25 22:36:50 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).
>> Best,
>> Lars
> 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. Thus we have to calculate the IR spectra 
> from dipole autocorrelation.

but surely an essential dynamics analysis of a long MD simulation will 
give you better results?

> Thanks to all of you for your help
> Christian.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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