[gmx-users] Different Coulomb energy between gromacs and my calculation

[Tanping Li]

Yes, I use Angstrom as the coordinate unit.



Tanping

--- David van der Spoel <spoel at xray.bmc.uu.se> wrote:

> On Wed, 2005-07-20 at 15:33 -0700, Tanping Li wrote:
> > Dear Gromacs users,
> > 
> > When I choose cutoff in Coulomb term, in my
> > understanding, if one pair is within cutoff, I can
> get
> > the exactly same result as Gromacs. I use
> formular:
> > 
> > e(i,j)=1389*q(i)*q(j)/r.
> the number 1389 is rounded and in strange units.
> Angstrom maybe?
> > 
> > 
> > But my test result from one charge group and one
> Na is
> > 6.250759; in gromacs, I set the step as 0, the
> result
> > is -6.252050.
> which number is this? what are you computing?
> 
> > 
> > It does not look like rundoff. This difference can
> be
> > enlarged in my real calculation between a certain
> > residue and waters.
> > 
> > How does gromacs calculate the coulomb interaction
> in
> > cutoff? Does it calculate between individual pairs
> and
> > fianlly get the sum?
> > 
> > Thank you very much. I tried all ways. It is
> really
> > hard to find the solution.
> > 
> > 
> > Tanping
> > 
> > 
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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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