[gmx-developers] LJ calculation

David van der Spoel spoel at xray.bmc.uu.se
Tue Dec 11 20:58:35 CET 2001

On Tue, 11 Dec 2001, sadhna wrote:

>            modifying the code for LJ calculation may not be trivial but i
>would like to look at it to see how difficult it is. Actually i am writing
>a set of programs and want to club them together as one. Among the
>programs that i am writing LJ calculation is one of them. I would like to
>know what logic has been used in classifying atoms into bonded and
>non-bonded. I have used one logic which seemed the only one possible to
>me,but its becoming too tedious(with many loops,strcmps ifs etc..) .So, i
>just wondered if a better alternative to it exists.
>Kindly also convey how and from where i can download the code.

After the configure steps etc. go to 
cd src/gmxlib
gmake innerc.c

this will generate the C-code for the inner loops where LJ interactions
are computed.

By the way, it's not quite clear what you want to do, but there is no
logic in this bit of the code which defines what is a bond and what not.
You have to do that beforehand, in the input files. If you want to do that
dynamically you basically have to do quantum mechanics.

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-developers mailing list