Re: AMBER: SANDER - Abnormal high velocities

From: David A. Case <>
Date: Wed, 28 Jan 2004 08:31:18 -0800

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 atom
> velocities and temperature control. From the very beginnig of the simulation,
> the velocities of the atoms are too high, and I can't find the reason. The
> starting structure was fully minimized previous to the MD run.
> ntt=1, tautp=0.2

This is way to short; try a value 5-10 times higher, and see if that helps.
(It is, however, likely that something else is wrong, but this is something
simple to try; also, set ntpr=1 when you have problems on very early steps,
and you might want to try to heat first to 100K or so.)

...good luck....dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Wed Jan 28 2004 - 16:53:01 PST
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