> my colleague is trying to simulate really big dendrimer molecule (diamete=
> r =20
> cca 100 A) and he needs
> to add 1411 counter ions. It seems that the default grid 1A is not the =20
> optimal value for such big system
> also taking in account calculated grid extends from solute cca 30 A so we=
> are on cca 2e6 grid points.
I'm not at all sure the grid extends 30A - if you want this, you should
check and maybe change the code.
>
> Tleap does not write any error but is seems that the calculation of "grid=
> charges" take very long time.
>
> So my question is. Is there any way how to reduce this time it means:
>
> #1
> To change default 1A grid to some more coarse, like 5A for example ?
See the code; should be possible.
> or
>
> #2
> To set some lower precision (less iterations) to speed up addions =20
> procedure ?
Not possible without avoiding recalculation of charges after
each ion placement.
> #3
> Is there eventually possibility simply to tell to addions procedure, =20
> please ignore
> electrostattic potential and place the ions randomly in the volume given =
> =20
> by the molecule + some extend ?
Not implemented, but shouldn't be hard to add. Maybe someone will do it :-)
Bill
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Received on Tue Apr 27 2010 - 10:30:03 PDT
