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 -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<<
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