Re: [AMBER] Amber and Short Bonds

From: Thomas Cheatham <>
Date: Mon, 26 Mar 2012 14:21:22 -0600 (Mountain Daylight Time)

> 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 - 13:30:03 PDT
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