Dear Bill,
thanks a lot for your prompt and complete reply !
I think might be reasonable to include into future LEAP versions
possibility to change default grid spacing (without code editing and
recompiling).
Just as the optional addions parameter.
Best wishes,
Marek
Dne Tue, 27 Apr 2010 19:01:36 +0200 Bill Ross <ross.cgl.ucsf.edu>
napsal/-a:
>> 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 - 11:30:03 PDT
