[gmx-users] NMA for a group

[Mark Abraham]

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