AMBER Archive (2008)

Subject: Re: AMBER: N(CN2)- ion

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Mon Dec 01 2008 - 08:47:14 CST

On Fri, Nov 28, 2008, babak minoofar wrote:

> I would like to do some MD simulation of N(CN2)- ion as a counterion of
> ionic liquid. I have optimized structure from ab initio calculation which
> looks like the attached pdb file
> But after MD pdb looks like this ....

How did you set up the force field used for the MD simulation? This is
probably going to require a lot of hand-work, since the bonding is so unusual.
Plus, the existence of linear N-C-N bonds makes it tricky to use standard
force field ideas. But without knowing what you have done so far, it's hard
to provide any good advice.

...dac

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