AMBER Archive (2003)

Subject: Re: AMBER: Constant temperature

From: David A. Case (case_at_scripps.edu)
Date: Sun Dec 28 2003 - 00:46:46 CST

On Sat, Dec 27, 2003, L Jin wrote:
>
> I ran the constant temperature MD at 300K just with minimization first and
> them MD. But I have seen that many users first heat their system from 0 to
> some temperature with first run by increasing the temp by say 10K gradually.
> Please anybody can tell me how did you do this? And the reason of doing
> this. Must I have this run for the MD? Thank you very much.

The use of "heating" as a form of equilibration is mostly historical. If you
have bad input coordinates (say from an older x-ray structure) it can help to
run some initial dynamics at relatively low temperatures to allow some of the
bad energies to be dissipated. But it is certainly not necessary, and many
people (including me) more typically now set tempi to the final temperature of
interest.

Is _is_ often important to use restraints on the solute (ntr=1) during
equilibration of the solvent. This keeps the system close to the starting
configuration while the temperature and density of the surrounding solvent
are equilibrated. Then the final stage of equilibration removes these
restraints.

The whole point of equilibration is to create a system independent of the
details of the starting configuration. There is no one "right" way to do
this.

..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
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