[gmx-developers] scaling 1-4 electrostatic interactions separately

[David van der Spoel]

chris.neale at utoronto.ca wrote:
> Hello,
> 
> I am wondering why there is a [ pairtypes ] section only for LJ and not 
> coulombic. I have been able to trick gromacs into properly combining two 
> forcefields that have a different fudgeQQ, but that trick is fairly 
> specific:
> http://www.gromacs.org/pipermail/gmx-users/2006-September/023761.html
Without looking things up you could use multiple pair interactions for 
each pair, but that will only help if one fudgeQQ_A = n * fudgeQQ_B with 
n integer.


> 
> I am in the process of writing up the results of my protein-lipid 
> simulations and I am currently trying to decide how to split the paper. 
> I would like to split the method plus proof-of-concept section out into 
> a simple one page methods letter but in that case I would need to 
> convince the reader that the method that I have used is necessary and 
> could not easily be replaced by a slight code modification to gromacs. 
> In fact this may be the case and is the reason why I am writing to this 
> list.
> 
> First: is there some important reason why a [ coulombic-pairtypes ] 
> section could not exist, or is it just that nobody has dedicated a day 
> of coding to make this happen? I figure that PME could make it more 
> difficult, but don't really know.
> 
> Second: is gromacs 4.x likely to allow users to arbitrarily set 
> coulombic 1-4 interactions in the same way that this can be done for LJ 
> 1-4 interactions by [ pairtypes ] ?

Section VIII of the gromacs 4 paper desribes very briefly the new 
tabulated bonded potentials. It could however be that there is not 
something like a Coulomb interaction, that multiplies a function by the 
charges (like there is for non-bonded potentials). Maybe Berk can comment.


> 
> I would like to emphasize that I am not asking anybody to do this. 
> Rather, I would like to understand how easy it would be to do and how 
> likely it is to be done since these answers will either motivate or 
> undermine a simple methods letter of the type that I have mentioned.
> 
> Thanks,
> Chris.
> 
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se