> 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
integrate...
Good luck.
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Received on Wed Nov 10 2004 - 00:53:00 PST
