[gmx-users] NMA for a group

Mark Abraham Mark.Abraham at anu.edu.au
Fri Jun 22 11:07:52 CEST 2007

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.


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