[gmx-users] question about [ pairs ] and interaction 1-4
alanwilter at gmail.com
Mon Jun 14 16:21:41 CEST 2010
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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