Re: [AMBER] H-Bonding and Amber's Shake algorithm

From: David A Case <case.biomaps.rutgers.edu>
Date: Mon, 23 Apr 2012 08:24:35 -0400

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 theĀ 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


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Received on Mon Apr 23 2012 - 05:30:04 PDT
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