AMBER Archive (2008)

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

From: babak minoofar (babak_minoofar_at_yahoo.com)
Date: Thu Dec 04 2008 - 10:00:58 CST

Dear David,
   Thanks for e-mail. I used gaff force filed for MD. After doing ab intio calculations and get I got prep file qnd then I made lib file then I used gaff force field to produce prameters file but I got message which said there angle na dihedral are missing. n1-c1-ne, c1-n1-cg-n1 which I used similar parameters force constant from gaff and angle from ab initio like:
type angle force constant
n1-c1-ne 173 120
c1-n1-cg-n1 1.1 180. 2.0 like X - X - X -X
With these changes I made the parameters and coordinate files qnd I run MD and I go so strange behvior of N(CN2) ion.
   Thanks
      Babak

> 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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