On Sat, Jun 06, 2009 at 02:06:56PM +0200, Florian Dommert wrote:
> * David van der Spoel <sp...@xray.bmc.uu.se> [2009-06-06 08:06:26 +0200]:
>> The VDW may work, but not differently scaled 1-4 and 1-5 coulomb
>> interactions.
>
> Where is the matter if I have a [ pairs ] directive in the itp file like
> this :
>
>
> [ pairs ]
> ; ai aj fu
> 1 5 2 0.5 -0.11 0.13 0.30250 0.095865
> 1 6 2 0.5 -0.11 0.13 0.30250 0.095865
> .
> .
> .
> .
> ;this is are nonbonded intramolecular IAs separated by more than theree
> bonds
> 2 5 2 7.569 0.07200 0.02300 0.00000 0.00000
> 2 6 2 7.569 0.07200 0.02300 0.00000 0.00000
I think this will work, but setting LJ parameters to zero will cancel
the interaction for these pairs. Is this what you intend to do?
I did a simple test: I've defined an abstract molecule like this:
X-X-X-X-X
so that 1 and fourth atom are 0.4 nm apart, and 1 and fifth atom
are 0.5 nm apart. I've set all bonded and non-bonded interactions to
zero, Nexcl=3, gen-pairs=yes, fudgeQQ=1.0, fugdeLJ=1.0.
Then I have defined [pairs] like this:
[ pairs ]
1 4 2 1.0 0.1 0.0215927 0.325052 0.25
1 5 2 1.0 0.1 0.0287903 0.433402 0.25
charges, sigma and epsilon are chosen in such a way that each
interaction should contribute exactly 1 kJ/mol. Indeed, the potential
energy calculated by GROMACS is 4 kJ/mol.
Now, changing the pairs to:
[ pairs ]
1 4 2 0.5 0.1 0.0215927 0.325052 0.25
1 5 2 0.8 0.1 0.0287903 0.433402 0.25
I get the potential energy of 3.3 kJ/mol, which means that coulomb14
whas rescaled from 1 to 0.5 and coulomb15 was rescaled from 1 to 0.8.
This is exaclty what I was looking for.
Thanks for all the comments,
Borys
--
REQUIMTE, & Molecular Modelling & Quantum Chemistry Group,
Department of Chemistry, & Institute of Physical & Theoretical Chemistry,
Faculty of Science, & Wroclaw University of Technology
University of Porto & http://ichfit.ch.pwr.wroc.pl/people/szefczyk
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