AMBER Archive (2003)

Subject: Re: question about temperature

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Mon Feb 03 2003 - 11:31:28 CST

the answer depends on the amber version.
For version 7, it adds all of the degrees of freedom
together and calculates the scaling factor.
There is one bath and one scaling factor for the entire
system, not just one target temperature. The exception
to this is that separate baths can be used with Locally
Enhanced Sampling (LES).
Carlos

----- Original Message -----
From: "Lishan Yao" <yaolisha_at_pilot.msu.edu>
To: <amber_at_heimdal.compchem.ucsf.edu>
Sent: Monday, February 03, 2003 12:02 PM
Subject: question about temperature

> Hi:
> From AMBER manual, I find that sander uses the same temperature
coupling
> constant
> for solvent and solute. My question is "Does sander count the temperature
> of solvent and solute separately, then scale both temperatures to target
> temperature by using the same coupling constant or sander just count the
> temperature of the whole system then scale the temperature to target
> temperature by using the same coupling constant for solvent and solute?"
> Thanks.
>
> Sincerely
> Lishan Yao
>
>