AMBER Archive (2009)

Subject: Re: [AMBER] POL3 & SHAKE

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Wed Jun 10 2009 - 14:11:40 CDT

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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