[gmx-users] NMA for a group

Christian Seifert cseifert at bph.ruhr-uni-bochum.de
Fri Jun 22 11:53:54 CEST 2007

On Friday 22 June 2007 11:07, Mark Abraham wrote:
> David van der Spoel wrote:
> > Christian Seifert wrote:
> >> Hi.
> >>
> >> Perhaps, I made a mistake in describing my problem. I can not believe,
> >> that no one ever tried this before.
> >>
> >> I have a phosphate in water and want to calculate the hessian just for
> >> the phosphate. How do I do that?
> >
> > there is a contradiction here in that you say the phosphate is in water
> > and you want to do the NMA for just the phosphate. Something like that
> > might work with a continuum solvent but I don't know how you would do it
> > with explicit solvent.
> Well you could just find the second derivatives of the energy with
> respect to the phosphate atomic coordinates numerically... but that
> doesn't sound like a good way to get numbers that mean anything.
> Mark

Yes, that is exactly what I want to do. Is there any keyword to calculate the 
hessian for a group of molecules/ a molecule in a large simulation system?


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