[gmx-users] Energy of part of system

[Mark Abraham]

Beniamino Sciacca wrote:
> I use interaction energy to estimate the interaction forces between the 
> molecules.... When the course of Potential (or DNA1-DNA2.......) is 
> constant, I use these values for estimate interaction forces. So I'm 
> using equilibrium value, isn't it?

My comment was half-joking, but I see you've got the wrong handle on 
something. If you're doing work on a system, i.e. pulling on a group, 
then it is not in equilibrium. Thus there's no problem with estimating 
interaction energies from such simulations, but they won't be 
equilibrium values.

Mark

> What can I do? is the file pull.pdo the only other way to estimate the 
> forces?
> Thanks
> Beniamino
> 
> Mark Abraham ha scritto:
> 
>> Beniamino Sciacca wrote:
>>
>>> Ok....
>>> another question: I use constraint pull code... is there some problem 
>>> in estimating interaction energy?
>>
>>
>> Only if you want equilibrium values :-)
>>
>> Mark
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