[gmx-developers] re: [gmx_developers] more about solvation free energy

[Erik Lindahl]

Hi,

>
> Yes, I realize how the parameters are set.  But what is the functional
> form treatment within this loop?  Infinite cutoff LJ and Coulomb
> interactions between just these atoms? Does the 1,4 routine assume
> things are fairly close together?

It's an explicitly listed interaction (i.e., no cutoff applied), but  
there's actually a safety-check that warns you if any 1,4  
interactions are further apart than twice the cutoff, or something in  
that ballpark (this is usually one of the first places where we  
notice a molecule is falling apart).

That's of course easy to remove if we want arbitrary pair interactions.

Cheers,

Erik


-----------------------------------------------------------
Erik Lindahl  <lindahl at sbc.su.se>     Backup address:  
<erik.lindahl at gmail.com>
Assistant Professor, Computational Structural Biology
Stockholm Bioinformatics Center, Stockholm University, SE 106 91  
Stockholm
Phone: +46 8 5537 8564     Fax: +46 8 5537 8214