On Wed, Jun 10, 2009, Hemant Gangwar wrote:
>
> I am using POL3 as my explicit solvent using amber10.
> manual suggest "minimization should be carried out without SHAKE".
> Now I have two question
> 1)Is it ok to allow to move H in rigid water models.
Not really.
> 2)When I tried minimization with(ntc=1,ntf=1),sander crashes but works
> fine with ntc=2
Without SHAKE, it is possible for electrostatic collapse to occur, where two
atoms end up on top of one another.
> if I use TIP3P,then it works fine even with ntc=1.
This may be a coincidence. My best suggestion: always use NTC=2. Your
minimizations won't go to completion, but you probably don't need them to.
Minimization of water is almost always just a prelude to MD anyway, and
doesn't need to find true minima.
...dac
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Received on Mon Jul 06 2009 - 08:36:31 PDT
