[gmx-users] aliphatic hydrocarbon parameters

[Erik Lindahl]

T. Zaraiskaya wrote:

>hello all,
>
>i am using LCH2 and LCH3 atom types introduced in ffG43a2x for lipid
>aliphatic chains;
>which function should i use for proper dihedrals in lipid chains?
>func 1 and gd_17 from ffG43a2xbon.itp or
>func 3 Ryckaert-Bellemans.?
>
Definitely Ryckaert-Bellemans. Actually, the Kuwajima potential is 
probably even slightly better, but that difference isn't large.

>
>
>2) ffG43a2x is it the same as 45A3 from  J.Comp.Chem. 22(11) 1205-1218 ?
>
No. The a2x isn't endorsed by the Gromos people in any way (and they 
shouldn't be blamed for possible errors). This was done as a diploma 
work a couple of years ago when there were no suitable lipid parameters 
in Gromos96 (I haven't tested the new a3 version, so frankly I can't 
tell which one producers more accurate results for membranes). Download 
the files from gromacs.org and study the README file for details about 
the parameterization.

Cheers,

Erik