[gmx-users] what does "Excluding 1 bonded neighbours for" mean?

David van der Spoel spoel at xray.bmc.uu.se
Thu Jan 31 10:52:37 CET 2002

On Wed, 30 Jan 2002, Rui Qiao wrote:

>Dear All:
>	I am running Gromacs and get the following information:
>processing topology...
>Excluding 1 bonded neighbours for Wall          1152
>turning all bonds into constraints...
>Excluding 1 bonded neighbours for Fld           3717
>turning all bonds into constraints...
>processing coordinates...
>	What does it means when saying "excluding # bonded neighbours for"
>. I did not define any bond in my system at all. In my system I have 1152
>wall atoms, and 3717 Fld atoms.
Could be just the atom itself. If you specify nrexcl 1 in your topology it 
will say this, whether or not there are actual bonds. Finally you can 
check your output topology by
gmxdump -s topol.tpr | less
and then search for exclusions:

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

More information about the gromacs.org_gmx-users mailing list