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.
> 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.
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