Re: AMBER: Heating POL3 Box Troubles

From: Thomas Steinbrecher <>
Date: Fri, 14 Mar 2008 14:22:21 -0700 (PDT)

Hi Paul,

ok, this is really beyond my expertise in Amber, but it *looks* like the
problem occurs in the dipole part, with the energy changing by an order of
magnitude between steps 82 and 83. This is suprising bc you said that with
ipol=0, the same problem occurs... Have you consulted section 5.7.5 of the
manual if your settings are correct? e.g. DIPMASS mentions that the
default value is meant for a 1 fs timestep.

> translate more or less as a single unit, with the exception of a few spots,
> where it seems like I have mini-blackholes. The nearby waters basically get
> sucked into a single point

Odd... I think it can be safely said that if you find out whats causing
this, you will have located the cause of the problem ;-)



Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA
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Received on Sun Mar 16 2008 - 06:07:46 PDT
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