[AMBER] Addions grid ?

From: Marek Maly <marek.maly.ujep.cz>
Date: Tue, 27 Apr 2010 16:59:16 +0200

Dear all,

my colleague is trying to simulate really big dendrimer molecule (diameter
cca 100 A) and he needs
to add 1411 counter ions. It seems that the default grid 1A is not the
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.

Tleap does not write any error but is seems that the calculation of "grid
charges" take very long

So my question is. Is there any way how to reduce this time it means:

To change default 1A grid to some more coarse, like 5A for example ?


To set some lower precision (less iterations) to speed up addions
procedure ?

Is there eventually possibility simply to tell to addions procedure,
please ignore
electrostattic potential and place the ions randomly in the volume given
by the
molecule + some extend ?

Thanks a lot in advance for any suggestion !

Best wishes,


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Received on Tue Apr 27 2010 - 08:30:03 PDT
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