[gmx-developers] short range energies

David van der Spoel spoel at xray.bmc.uu.se
Tue Mar 26 15:17:41 CET 2002

On Tue, 26 Mar 2002, Mehmet Suezen wrote:

>> One more thing: in ns.c (or force.c) an array is made bHaveLJ for atoms to
>> see whether LJ interaction should be computed. You may have to set these,
>> oterwise the neighboursearcher will not put atom pairs in the
>> neighbourlist.
>as far as I've seen in ns.c in function search_neighbours(), how it puts
>particles in to list if one choose bham for example? Or, how could one
>be sure
>that neighborlist constructed properly?
I should have thought of this before: if you set an environment variable
setenv DUMP_NL 1
it will dump the entire neighbourlist in your md.log file, so you can 
check whether all interactions are there. The format is a bit terse, 
please check the source in wnblist.c

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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