[gmx-users] question about [ pairs ] and interaction 1-4
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 Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> gmx-users mailing list gmx-users at gromacs.org
> 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users