[gmx-users] Scaled 1-5 interactions

[Borys Szefczyk]

On Sat, Jun 06, 2009 at 02:06:56PM +0200, Florian Dommert wrote:
> * David van der Spoel <spoel at 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