[gmx-users] NMA for a group

Christian Seifert cseifert at bph.ruhr-uni-bochum.de
Fri Jun 22 12:27:40 CEST 2007

On Friday 22 June 2007 10:59, Bert de Groot 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.
> right. one way to include water and still have a manageable system size is
> to work with a small droplet of explicit water.
> Bert

The hessian is the second (numerical) derivative of the atoms in the three 
dimensions. In the future, I want to calculate the hessian of molecules next 
to proteins, so the "small droplet of explicit water" will not work here.  I 
do not understand, why I need to calculate the second derivatives of the 
atoms of the whole system, if I just need it of a small molecule.


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