Date: Sun, 12 May 2013 15:38:51 -0400
For what it's worth, attached are some fun screenshots. Mg2+ is in orange.
On Sun, May 12, 2013 at 3:34 PM, Jonathan Gough
<jonathan.d.gough.gmail.com>wrote:
> Dear All,
>
> I got the NaN error in my restart file while running accelerated MD in
> TIP4Pew. That lead me to run my aMD simulation printing every step
> (ntpr=1, ntwx=1). A careful examination of the trajectory shows one of the
> Mg2+,
> (using the previously posted paramaters labeled Oelschlaeger et al JMB
> 2007 Mg dummy
> http://archive.ambermd.org/201202/0429.html )
> over the course of a few frames, has some very weird "motion" as if it's
> stretching (it has an octahedral conformation) when close to an
> un-protonated ASP. this then leads to atoms on the ASP jumping out to
> infinity as well as one of the Mg+2 jumping out as well, followed by
> everything disappearing.
>
> FWIW, I managed to minimize, heat, equilibrate the density (10 ns),
> equilibrate (10 ns) before starting the aMD. Parallel experiments included
> the same system with 2 Mg2+, 1 Mg2+, and no Mg. the one with a single Mg,
> survived the aMD run for a longer period of time, but eventually gave me
> the same error.
>
> therefore I am concluding, for the moment, that this is likely an issue
> related to the Mg2+ atom's and associated parameters.
>
> Searching lead me to find the following message from Ross
>
> *http://archive.ambermd.org/201210/0481.html*
> *
> *
> I believe saying, there is an issue with atoms with small (no) VDW radii
> collapsing when they get in close proximity to highly charged atoms.
>
> However, the ASP was not protonated.
>
> All that being said, i am not exactly sure how to rectify the problem.
> 1) revert to the old Mg2+ paramaters?
> 2) change something with these?
>
> Can anyone provide some insight?
>
> Using:
> AmberTools version 13.02
> Amber version 12.16
>
> Thanks,
> Jonathan
>
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(image/png attachment: Screen_Shot_2013-05-12_at_3.25.09_PM.png)
(image/png attachment: Screen_Shot_2013-05-12_at_3.24.25_PM.png)
(image/png attachment: Screen_Shot_2013-05-12_at_3.25.32_PM.png)
