[gmx-users] treecode again

[David]

On Mon, 2004-05-03 at 10:06, Mu Yuguang (Dr) wrote:
> Dear David, Eric,
> If one really want to implement his treecode method into gromacs, which
> part of code should be modified ?
> Can you give some advices in advance ?
The tree code comes in place of long range electrostatics, right? In
that case you should have a call to the treecode algorithm from the
force subroutine (mdlib/force.c). Just put it in place of e.g. the PPPM
code, then if you choose PPPM  in the mdp file your treecode will be
executed. 

For a single processor it is not more complicated than that, for
parallel processing it probably is.


> 
> Thanks 
> Regards,
> Yuguang
>  
> Dr. Yuguang Mu
> School of Biological Sciences
> Nanyang Technological University
> Singapore 637616
> Tel: 0065-67906489
>  
> 
> -----Original Message-----
> From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]
> On Behalf Of Erik Lindahl
> Sent: Friday, April 30, 2004 5:02 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Mailing list issue fixed
> 
> Hi,
> 
> Not a lot (if anything) for today's typical biological problems since 
> the effective interactions are almost always dipole-dipole (or decaying 
> even faster), so we can use fairly short cutoffs.
> 
> However, that doesn't mean it wouldn't be useful - I could imagine 
> large (simplified) membrane systems or other setups where it would be 
> much faster...
> 
> Cheers,
> 
> Erik
> 
> 
> On Apr 30, 2004, at 10:39 AM, Mu Yuguang ((Dr)) wrote:
> 
> > To what degree that you guys think, a well-developed, so-called,
> > treecode algorithm for N-body problem can improve our MD simulation
> > speeds ?
> >
> >
> > Regards,
> > Yuguang
> >
> > Dr. Yuguang Mu
> > School of Biological Sciences
> > Nanyang Technological University
> > Singapore 637616
> > Tel: 0065-67906489
> 
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-- 
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://xray.bmc.uu.se/~spoel
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