On Mon, Apr 23, 2012, Adam Jion wrote:
>
> I'm simulating a system of cyclic-dimers in solution.
> Presumably, H-bonding is important for dimerization
> However, as I'm using the tip3p model for water, I'm also using the
> SHAKE algorithm (i.e. ntc = 2, ntf =2) for my simulation.
> Will the use of Amber's SHAKE algortithm affect H-Bonding between 2 molecules?
No..You *must* use SHAKE if you are using tip3p water....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 23 2012 - 05:30:04 PDT
