[gmx-developers] tabulated bonded potential in CVS

Berk Hess hessb at mpip-mainz.mpg.de
Mon Aug 27 14:10:50 CEST 2007

Lu Lanyuan wrote:

> Hello,
> I'm wondering if anyone has tested the tabulated bonded potential
> function in CVS version (VERSION 3.3.99_development_20070720).
> I was trying a united atom methanol case in the "tutor/methanol"
> directory. I changed the Me-O bond from [ bonds ]
> ; ai aj funct c0 c1
> 1 2 1 0.13600 376560.
> to
> [ bonds ]
> ; ai aj funct c0 c1
> 1 2 8 376560. 0
> And I calculated the u(r) and -u(r)' using the formular:
> u(r)=0.5*(r-0.136)^2 -u(r)'=-(r-0.136)
> Thus I built my table_b0.xvg as three columes r,u(r),-u(r)'. I was
> using a r space 0.002 nm and r range 0-1 nm.
> But every time I got "Segmentation fault" and couldn't run my
> simulation. I tried the same input files without tabulated bonded
> interactions and it worked fine. Is this a bug or just because the
> tabulated bonded potential code is not completed?
> I do appreciate it if anyone can give me some hints.
> Lanyuan Lu
> Department of Chemistry
> Uinversity of Utah
I implemented the tabulated bonded potentials and for me, as well as my
they work fine.

Could you file a bugzilla report?


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