[gmx-developers] scaling 1-4 electrostatic interactions separately
chris.neale at utoronto.ca
chris.neale at utoronto.ca
Sat Mar 8 20:39:47 CET 2008
Quoting David van der Spoel <spoel at xray.bmc.uu.se>:
> chris.neale at utoronto.ca wrote:
>> 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:
> 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.
Thank you for your comments. This is exactly what I have done. Where
fudgeQQ_A = 0.5 (opls) and fudgeQQ_B = 1.0 (lipids). I then specify [
pairtypes ] for group B as half of what they should be and include the
1-4 pairs twice for group B, while setting fudgeQQ = 0.5. At first
glance it is simple enough to warrant only a single sentence in a
methods section, but I had to test it since one can imagine that a
second pair might overwrite the first or something else unexpected
since I don't think that gromacs was coded with this usage in mind. In
fact it works perfectly with the only difference being rounding errors
from slightly different mathematical form (two calculations instead of
>> 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
Thanks for pointing this out. I did take a look at this section, but
didn't find any particular mention here for exactly what I am
describing. For other readers, the section referred to reads:
"User defined nonbonded interactions that can be assigned
independently for each pair of charge groups were already supported,
and we have now additionally implemented user defined bonds, angles,
and dihedrals functions."
It would be great if you could comment here Berk.
Thank you again,
>> 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.
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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
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