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

Mark Abraham mark.abraham at anu.edu.au
Tue Jun 15 03:14:28 CEST 2010

----- Original Message -----
From: Alan <alanwilter at gmail.com>
Date: Tuesday, June 15, 2010 0:22
Subject: [gmx-users] question about [ pairs ] and interaction 1-4
To: Gromacs <gmx-users at gromacs.org>

> 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.

I think p112 implies that the [pairs] entries will look for parameters in [atomtypes], complain and use zeroes if lacking, and then apply fudges.

You could compare the results with [pairs] parameters explicitly set to zeroes.

> 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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