AMBER Archive (2009)

Subject: Re: [AMBER] help with TIP4P and mpi pmemd

From: case (case_at_biomaps.rutgers.edu)
Date: Fri Dec 04 2009 - 15:16:22 CST

On Fri, Dec 04, 2009, Hashem Taha wrote:

>
> Constant Volume Minimization
> # Control section
> &cntrl
> ntwx = 50, ntpr = 1, ntwr = 1,
> scnb = 1.0, scee = 1.0, nsnb = 25, dielc = 1, cut = 8.0,
> ntb = 1,
> maxcyc = 1000, ntmin = 0, dx0 = 0.01, drms = 0.0001,
> ntp = 0,
> ibelly = 0, ntr = 1,
> imin = 1,
> &end
> Group Input for restrained atoms
> 5.0
> RES 1 2
> END
> END

You are running TIP4P minimization without turning on SHAKE. This is
quite dangerous, since this is a rigid water model, and can do funny things
(e.g. head towards negative infinite energies) if the bonds are allowed
to change their lengths. Can you see if the problem persists with SHAKE
turned on?

[FWIW: I went to $AMBERHOME/test/tip4p and turned one of the MD runs
into a minimization run, and didn't see any problems. But the problems well
could depend on details of your run.]

...dac

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