[gmx-users] Re: Re: Re: Re: Does GMX compute coulomb interaction between oxygen and hydrogen in SPC water model?

Mark Abraham Mark.Abraham at anu.edu.au
Mon Oct 26 01:58:44 CET 2009

xuji wrote:
> Hi
> Thank you for your advice and sorry for disturbing you agian.
> I read the cooresponding relevant manual sections, I've known
> how to get the parameters of the tabulated funcionns.
> But how much is the difference between the direct computation
> and the table lookup method is?
> For example, I simulated a box of water. The results of tabluted
> and simple cut-off method of coulomb interation differ a lot.

... then the function in the table was not 1/r if the cut-offs were the
same, or your comparison metrics were not valid, or your simulations
were not equilibrated, or if equilibrated they were too short.

> And is it right to use simple cut-off coulobm fuction
> conjunction with the PME method to get the whole coulomb
> contribution?

You can't use simple cut-off with PME, because the latter modifies the
short-range interactions, as you can see in manual 4.9. If you choose
PME, you will transparently use tables that look up the modified
interactions, because these are faster.

It's very easy to construct (garbage in => garbage out) systems in
computational chemistry. Read first!


> 2009-10-26
> ------------------------------------------------------------------------
> Ji Xu
> The State Key Laboratory of Multiphase Complex System
> Institute of Process Engineering
> Chinese Academy of Sciences
> Beijing 100190, China
> Tel.: +86 10 8262 3713-804 
> ------------------------------------------------------------------------
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