[gmx-developers] modifing nonbonded interactions

[Mark Abraham]

Nazish Hoda wrote:
>> PME requires periodicity, which you shouldn't need for implicit-water.
> There are still charged molecules in the neighboring, next neighboring, etc
> boxes.
> How to account for them ?  

If your system has a net charge, you have even more problems if you 
require no solvent (so no counter-ions) and periodicity. PME doesn't 
work for systems with net non-zero charge.

>> If you're really wanting to do implicit-water simulation, you should be 
>> looking at simulation packages other than GROMACS.
> 
> Won't using a modified LJ parameters work ?

Life is not that simple. These parameters are carefully optimized to 
reproduce some (often vaguely) relevant data. It's inconceivable that 
any form of 6,12 potential on solute atoms could account for the 
electrostatic, frictional, thermostatic, dispersion and doubtless other 
effects that explicit solvents have upon their solutes. See 
http://wiki.gromacs.org/index.php/Parameterization

Mark