AMBER Archive (2003)

Subject: Re: AMBER: separate thermostats for different molecules

From: David A. Case (case_at_scripps.edu)
Date: Tue Aug 05 2003 - 00:19:02 CDT

On Mon, Aug 04, 2003, Arvid Soederhaell wrote:
>
> I wonder if it is possible to use separate thermostats for different parts
> of a simulation? I have a membrane simulation that runs relatively nice,
> but I have the impression that the lipids are much colder than the
> surrounding water. I have not actually measured the temperature in the
> different parts of the box, but the lipids are terribly well ordered and
> it looks like gel phase, rather than liquid crystaline phase.

As you note, we don't have separate temperature baths. This feature may
reappear in the next release.

You could try the Andersen-type temperature coupling (see the vrand variable).
That should more directly force all parts of the system to be at a particular
temperature.

..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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