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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Received on Sun May 12 2013 - 13:00:02 PDT
