[gmx-users] some things I am wondering

David van der Spoel spoel at xray.bmc.uu.se
Wed Aug 21 14:43:00 CEST 2002

On Wed, 2002-08-21 at 13:44, zpxu wrote:
> and I will be very happy if you tell me why.
> 1) in the section [moleculetype], we must specify the value of nrexcl(excluded numbers)
>     In my understanding, non-bond interactions within the number of bonds are excluded.
>     so if using bond+angle+dihedral, nrexcl will be set to be 3, and if using bond+angle only,
>     I need only set it to be 2, it is right? for the result of 2 and 3 are quite different.
This is force field dependent. Some force fields have dihedrals and non
bonded interactions between 1-4 atoms. 

> 2) why we must specify the atom number with bond, and angle interaction in the [bonds] and [angles]
>    section? because in some cases, if the atoms have great displacement, the bond and angle list 
>    have to be updated, and so I guess the GROMACS have the bond list finding function. but why we 
>    must specify it at the topological file?
If the atoms move too far apart such that there are no bonds anymore
something else is wrong. It shouldn't happen.

> thank for answering suck fundamental questions.
Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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