[gmx-users] Coulomb 1-4 interactions

Ryogo Sugitani rsugitani at gmail.com
Fri Sep 8 19:41:57 CEST 2006


What is your fudgeQQ value in ffamberXX.itp?
This value (I think the default is 0.8333) should be the reciprocal of 
scaling factor used in Amber's input file (I think the default is 1.200).
Check amber's manual specific parameter name for it. (I don't remember off my head right now.)



On Fri, 8 Sep 2006 13:26:45 -0400, Jianhui Tian wrote:
> Hi gmx-users:
> I am running a comparison between AMBER and Gromacs for a AOT system. 
> First I created the AMBER force field and then transformed it to 
> Gromacs force field. I did 1 step of MD respectively in AMBER and 
> Gromacs with the same configuration. All the energy terms including 
> bond, angle, dihedral, LJ (SR), LJ (14) and Coulomb (SR) are the same 
> with each other between the two runs except the Coulomb (14) 
> interaction. What might be the reason for this? I have totally no 
> idea. Because the LJ (14) and Coulomb (14) calculation use the same 
> 1-4 pairs in Gromacs, the LJ (14) is the same which means the 1-4 
> pairs are the same between AMBER and Gromacs. The Coulomb (SR) is the 
> same which means the charges are the same between AMBER and Gromacs. 
> (I also checked these two things explicitly between AMBER and 
> Gromacs.) How could the Coulomb (14) be different then? Does any one 
> have any idea about how the coulomb (14) interactions are calculated 
> in AMBER and Gromacs? Thanks a lot.
> Best Regards,
> Justin
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