[gmx-users] Scaled 1-5 interactions

[Florian Dommert]

* Borys Szefczyk <szefczyk at mml.ch.pwr.wroc.pl> [2009-06-07 14:12:14 +0200]:

>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?

Glad to hear the my help works. Setting the LJ parameters zero for the
should avoid a further contribution of the LJ part from the defined 1-5
IA, since they are already present in the nonbonded part of the
interaction types. Accoring to Chapter 5.3.4 of the manual, the [ pairs ]
directive allows to add further nonbonded energy terms within a molecule.
This is exactly the goal we want to achieve ;)

Cheers,

Flo

>
>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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-- 
Florian Dommert
Dipl.-Phys.

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

Tel: +49 - 711 / 6856-3613
Fax: +49 - 711 / 6856-3658

EMail: dommert at icp.uni-stuttgart.de
Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert

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