AMBER Archive (2009)

Subject: Re: [AMBER] unexplained blow-up at restart

From: Sally Pias (
Date: Fri Jul 10 2009 - 13:59:24 CDT


It sounds like you may have identified the problem, as the only thing
I noticed in visualizing the md2_NPT trajectory is that the molecule
shifts over (translates) noticeably at step 1. That is why I tried
the Langevin thermostat, as I thought it might be a "flying ice cube"
effect. I will try setting ntcm to 0.

Many thanks,


On Fri, Jul 10, 2009 at 11:58 AM, Carlos
Simmerling<> wrote:
> Sally- I got your files.
> can you redo rune after changing ntcm to 0, and also try switching back to
> Berendsen thermostat (ntt=1)?
> try them separately. it may be that in run2 the molecule was recentered, and
> the refc was not. in general combining positional restraints with removal of
> center of mass motion can be dangerous. we have better checks in more recent
> versions of Amber
> carlos

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