> Also, make sure you haven't drastically increased the bond force
> constants. The values used are right at the edge of stability. The fact
> that you have to go to shorter time steps suggests that you boosted the
> force constants for some reason...
Hello,
no, the force constants are those of "normal" bonds, standard values of CT-CT and CT-HC. The only thing I've changed is the equilibrium bond length.
________________________________________
From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] on behalf of Thomas Cheatham [tec3.utah.edu]
Sent: 26 March 2012 21:21
To: jason.swails.gmail.com; AMBER Mailing List
Subject: Re: [AMBER] Amber and Short Bonds
> The equilibrium bond distances should have little effect on the
> stability of your simulation, I would think. You don't have to worry
> about VDW and EEL clashes between bonded pairs (since those interactions
> are excluded from bond/angle partners).
Also, make sure you haven't drastically increased the bond force
constants. The values used are right at the edge of stability. The fact
that you have to go to shorter time steps suggests that you boosted the
force constants for some reason...
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Received on Mon Mar 26 2012 - 16:30:03 PDT
