----- Original Message ----- From: Alan <alanwil...@gmail.com> Date: Tuesday, June 15, 2010 0:22 Subject: [gmx-users] question about [ pairs ] and interaction 1-4 To: Gromacs <gmx-users@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. Mark > 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<< > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search > before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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