[gmx-users] bonded pairlist

David spoel at xray.bmc.uu.se
Wed May 21 20:38:01 CEST 2003

On Wed, 2003-05-21 at 19:12, Fan Hao wrote:
> Hello, gmx developers:
> 	I want to make sure about my understanding of bonded pairlist
> in gmx. I think for bond stretching, angle, dihedral and improper
> dihedrals, gmx put the first, second and third neighbour lists
> in t_iatom type array, is it true? Also I hope to know what identifier 
> was used to recognise different interations. For example, How can I 
> get the 1-4 interaction neighbourlist?
> 	Thanks a lot in advance!

there are separate lists for all interactions, although it can also be
recognized from the type of the interaction. Each of the interactions is
stored as (for e.g. angles)
type ai aj ak type ai aj ak type ai aj ak

Where type is an index in the parameter array (idef->iparams)
Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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