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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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