[gmx-users] genion II

Erik Lindahl lindahl at stanford.edu
Fri Mar 8 20:18:46 CET 2002

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.
>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 



More information about the gromacs.org_gmx-users mailing list