AMBER Archive (2004)

Subject: Re: AMBER: single strand simulation

From: Thomas E. Cheatham, III (
Date: Tue Nov 09 2004 - 18:32:58 CST

> I'm using Amber7 to do a MD simulation of a single strand DNA with a
> modified base in explicit water. The protocol is same as DNA tutorial on
> Amber website, except using ntt=1 for temperature control. But the
> simulation got error termination with vlimit and shake problem. Any
> suggestion is appreciated.

> NITER, NIT, LL, I and J are : 0 2 74 240 241

Are atoms 240 and 241 in the modified base? Make sure that your modified
base parameters is not adding a significantly higher frequency (larger
force constant) bond interaction. Otherwise, make sure that the system
was minimized prior to performing MD (without restraints). SHAKE and VMAX
failures are usually evidence of a hot spot. This could be due to a bad
geometry leading to large forces and much motion or force constants that
are too high leading to vibrations too fast for the integrator to

Good luck.

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