AMBER Archive (2003)

Subject: Questoin about temperature

From: Maverick (louhongf_at_msu.edu)
Date: Fri May 02 2003 - 00:27:29 CDT

Hi:
I am trying to calculating water's temperature by caculating the water's
freedom and total kienetic of all atoms belonging to water.
The water's freedom is got by 6*# of water(i.e 3 bonds are considered). The
simulation temperature is 303K and has one protein in it.
I compare the results with what sander outputed. My temperature is about
310K which is a bit higher than the amber's output. It is true that maybe
the temperature of the protein is lower than 303K. But I calculate protein's
temperature. It is also about 310K. So apparently there is something wrong
in my calculation.

Could you give some suggestion what's wrong with the calculation!

Hongfeng Lou
Have a nice day!