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
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