[gmx-users] NMA for a group

[David van der Spoel]

Christian Seifert wrote:
> 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.
> 

but what does it mean if you would be able to do that? You would get the 
hessian of the molecule in a constant field of solvent and protein. your 
are probably better off doing an MD simulation and running essential 
dynamics, then the effect of the environment is explicitly taken into 
account, and you will have much more realistic motions. It is like the 
difference between gas phase spectroscopy in  a complicated field, and 
liquid phase spectroscopy.


-- 
David.
________________________________________________________________________
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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