[gmx-users] NMA for a group
Mark.Abraham at anu.edu.au
Fri Jun 22 11:07:52 CEST 2007
David van der Spoel wrote:
> Christian Seifert wrote:
>> 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.
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