AMBER Archive (2009)

Subject: RE: [AMBER] ntt=3 and ibelly=1

From: Ross Walker (
Date: Thu Jul 16 2009 - 22:44:47 CDT

Hi Kristina,

Yes this makes sense since the langevin equation does not make sense if you
freeze some of the atoms. I guess we should have a trap that prevents the
use of ntt=3 with ibelly=1. I will add it to the development version so
future versions will not allow this option.

All the best

> -----Original Message-----
> From: [] On
> Behalf Of Kristina Furse
> Sent: Thursday, July 16, 2009 9:07 AM
> To: AMBER Mailing List
> Subject: [AMBER] ntt=3 and ibelly=1
> Hi all-
> I just did something stupid that cost me time and energy, so I thought
> I'd share it in the hopes it might prevent someone else from doing the
> same.
> I've run a number of regular, explicit DNA simulations, and wanted to
> do some frozen DNA simulations, using ibelly=1, for comparison. I chose
> a set of snapshots, centered the DNA, imaged the water and ions around
> it, then did a quick minimization (250 steps) to clean up any
> instantaneous weirdness in the DNA structure since I was going to
> freeze it. I run my simulations NVE, but did some NVT equilibration to
> re-establish the temperature for the water and ions with the DNA
> frozen. That was my problem--in my general equilibration protocol, I
> use Langevin dynamics, ntt=3. Apparently this is not compatible
> w/belly. My DNA atoms still got kicked around during the equilibration
> even though the moveable belly only included water and ions. I ended up
> with hydrogens frozen in very strange positions for my subsequent NVE
> trajectories. Temps and energies looked fine--bond and angle energy
> didn't show up in the output b/c of belly--so I only caught it by
> visualizing the trajectory to hunt down a different problem.
> So, long story short, no ntt=3 with ibelly=1, unless I'm missing some
> other flag or setting that would have rescued the plan.
> Kristina
> --
> Kristina Furse
> Postdoctoral Research Associate
> 260B Stepan Chemistry Hall
> Notre Dame, IN 46556
> (574)631-3904
> _______________________________________________
> AMBER mailing list

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