Re: AMBER: N(CN2)- ion

From: David A. Case <>
Date: Mon, 1 Dec 2008 09:47:14 -0500

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.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
Received on Fri Dec 05 2008 - 18:22:00 PST
Custom Search