[gmx-users] question about [ pairs ] and interaction 1-4

Alan alanwilter at gmail.com
Mon Jun 14 16:21:41 CEST 2010

Hi there,

I mostly use ffamber and sometimes I look in oplsaa to understand how things
are implemented in gromacs (4.0.5)

I have an example here, where 2 atoms, in a phosphate (see
http://en.wikipedia.org/wiki/File:1-hydrogenphosphate-3D-balls.png) in 1-4
interaction that have opposite charges (0.473 x -0.787) and when doing a EM,
the H will move towards and basically join one of the Oxygen of the
phosphate (coulomb force clearly acting, but no LJ repulsion?).

The definitions in the top file are:

[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
1               2               yes             0.5     0.8333

[ pairs ]
;   ai     aj    funct
     1      4      1 ;    HHO - O01

What I was expecting is since I declared the pair 1, 4 in [ pairs ]  and the
parameters to be set 0 by omission (or am wrong here?) that such interaction
between atoms HHO and O01 shouldn't happen, but clearly it's not what I see.

Yet I checked the manual, page 112 in particular.

It is the first time I come across an example where I have 2 atom in 1-4
interaction with such a large opposite charges.

Is the behaviour I see OK, although apparently rare?

Many thanks in advance,

Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
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