AMBER Archive (2003)

Subject: Re: Minimization problem w/ counter-ion !

From: Marco Preto (mcpreto_at_fc.up.pt)
Date: Wed Oct 30 2002 - 13:11:58 CST

Thank you, Prof. Case, for your exact and quick response!
Indeed, that was the problem!

David A. Case wrote:

> On Thu, Oct 31, 2002, Marco Preto wrote:
>
>> I'm trying to run a minimization of a solvent box (with my solute and
>> Cl- fixed) to get a better starting point to the equilibration dynamic
>> run of my system. Unfortunatly I'm having trouble with the electrostatic
>> interactions (this value goes to so negative magnitude that the format
>> is not suficient to writ it and my output comes like ***********. I've
>> tryed to put the counter ion using addions and when that did not work I
>> tryed to put it manually on my system, in diferent positions, but the
>> calculations allways stoped with a segmentation fault, during this
>> minimization.
>>
>> &cntrl
>> imin=1, maxcyc=200000, cut=12, igb=0,
>> ntb=1, ntpr=1000, ncyc=2000,
>> ibelly=1, ntwx=100,
>> &end
>> Group input for moving atoms
>> RES 10 3846
>> END
>> END
>>
>>
>> Res 10 to 3846 are my water molecules!
>
>
> The problem most likely is that you are not using SHAKE for your waters; you
> *must* set ntc=ntf=2 to use the TIP3P water model, otherwise you will get
> exactly the behavior you describe: the O-H bonds in the water can stretch, and
> lead to "fusion" betwee the hydrogens (which have no vdW radii in this model)
> and other charges (like those of the counterions.)
>
> Second, why are you running 200000 steps of minimization? I'd suggest a value
> somewhere between two and three orders of magnitude smaller.
>
> ..hope this helps...dac
> 

-- 
_____________________________________________________________________
 Marco A. C. Preto               |"Quantum temporis lucratur qui non
 PH.D. student                   |aspicit quod vicinus dicit, agit
 Theoretical Chemistry group     |vel cogitat, sed tantum quod ipse
 Chemistry Deparmant - FCUP      |agit ad id iustum et sanctum 
 Porto, Portugal                 |reddendum"
_________________________________|
                                 |   from my homonimous
email: mcpreto_at_fc.up.pt          |  
                                 |                 Marcus Aurelius
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