AMBER Archive (2004)

Subject: Re: AMBER: SANDER - Abnormal high velocities

From: Carlos Simmerling (
Date: Wed Jan 28 2004 - 10:36:45 CST

also try heating from something other than 0K -
any small problem gets amplified too much when
you scale the velocities this much. Maybe 100K to 298K
would work better. That's been my experience-
starting from 0K can be very dangerous.

> On Wed, Jan 28, 2004, Miguel de Federico wrote:
> >
> >
> > I'm trying to run a MD in vacuum heating from 0K to 298K in 20ps. I
used one
> > imput file I had used succesfully, but now there is someting wrong with
> > velocities and temperature control. From the very beginnig of the
> > the velocities of the atoms are too high, and I can't find the reason.
> > starting structure was fully minimized previous to the MD run.
> >

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