AMBER Archive (2009)

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

From: Kristina Furse (Kristina.Furse.1_at_nd.edu)
Date: Thu Jul 16 2009 - 11:07:23 CDT

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
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