[gmx-users] genion II

[Erik Lindahl]

Pedro Alexandre de Araujo Gomes Lapido Loureiro wrote:

>Citando Erik Lindahl <lindahl at stanford.edu>:
>
>>Hi Pedro,
>>
>>This isn't really an answer to your questions, but when I need to insert 
>>new particles I usually use free energy runs with softcore interactions 
>>and "grow" the ion from a zero-type particle without charge or LJ 
>>interactions to the real atom type and charge of the ion.
>>
>>This usually works well with larger molecules, like peptides and 
>>cholesterol, too.
>>
>>Cheers,
>>
>>Erik
>>
>>
>Thank you (once more!), Erik.
>
>In fact, genion exchanges a water molecule for an ion (and so, I am not 
>really "inserting" a particle, am I ?).
>
Yes, that's right, but the neighboring waters will still have to orient 
themselves with the hydrogens pointing towards the Cl-, and that part is 
much easier to do with free energy molecular dynamics than energy 
minimization!

Cheers,

Erik