AMBER Archive (2004)

Subject: Re: AMBER: SANDER - Abnormal high velocities

From: David A. Case (case_at_scripps.edu)
Date: Wed Jan 28 2004 - 10:31:18 CST

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:      case_at_scripps.edu
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            |    http://www.scripps.edu/case
==================================================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu