[gmx-developers] Re: Force calculation

[David van der Spoel]

Chenyue Xing wrote:
> Hi David,
>  
> I actually tried with a 3-atom system first and that worked perfect. 
> Then I tried a larger system which now has the segfault problem. My 
> conformation is good at least for normal interactions and the fz only 
> case. Maybe there's some conflict or inconsistency when I do a r=z case?
> As the huge r first appeared in the 4th step (I suspected there's 
> inequilibrium in the system), I used a more frequent nblist update to 
> see if it can avoid that but no luck. And a nblist_update freq=1 gives 
> stuck (infinite loop somewhere maybe?). So would you come across any 
> guess that I might unfortunately do anything bad with the neighborlist 
> codes (I haven't modified the neighborlist codes though).
>  
The neighborlist code works in 3D as well and particles that are close 
in z may still fall outside the neighborlist, unless you use an infinite 
one, which is not possible if you have PBC.


> Thank you very much!
> Chenyue
> 
>  
> On 10/17/06, *David van der Spoel* <spoel at xray.bmc.uu.se 
> <mailto:spoel at xray.bmc.uu.se>> wrote:
> 
>     Chenyue Xing wrote:
>      > Hi David,
>      >
>      > I want to use just a LJ potential for a z-dependent only
>     interaction. I
>      > noticed that 1/r^n and 1/r^(n+1) are used for energy and force
>      > calculation so I tried to set r = z only.
>      >
>      > Hope you can give me more advices.
>      > Thank you very much!
>      >
>      >
> 
>     I don't see why it shouldn't work, except when your starting
>     conformation is bad (or a programming error of course). Try with a two
>     particle test system first.
> 
> 
>     --
>     David.
>     ________________________________________________________________________
> 
>     David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>     Dept. of Cell and Molecular Biology, Uppsala University.
>     Husargatan 3, Box 596,          75124 Uppsala, Sweden
>     phone:  46 18 471 4205          fax: 46 18 511 755
>     spoel at xray.bmc.uu.se
>     <mailto:spoel at xray.bmc.uu.se>    spoel at gromacs.org
>     <mailto:spoel at gromacs.org>   http://folding.bmc.uu.se
>     ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
>     _______________________________________________
>     gmx-developers mailing list
>     gmx-developers at gromacs.org <mailto:gmx-developers at gromacs.org>
>     http://www.gromacs.org/mailman/listinfo/gmx-developers
>     Please don't post (un)subscribe requests to the list. Use the
>     www interface or send it to gmx-developers-request at gromacs.org
>     <mailto:gmx-developers-request at gromacs.org>.
> 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-developers-request at gromacs.org.


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++