I’m simulating water using SPCE model and I used regions to compute the spatial temp profile. the water box is thermostated by Noose hoover at 300 K. While a temperature of specific bin printed out via temp/region, it gives some temperature around 200 K or so, What is the problem with compute temp region?

no problem. this is to be expected. you are using shake

to keep your waters rigid. that removes three of the nine

degrees of freedom that you have with three atoms. check

out this segment of the documentation:

Thanks Alex, Is there any correlation between N (number for extra) and the number of molecules in the region/bin? Because I tried 3, -3 , there was no change to the temperature.

Thanks Alex, Is there any correlation between N (number for extra) and the

number of molecules in the region/bin? Because I tried 3, -3 , there was no

change to the temperature.

of *course* there is a correlation between the number of DOFs removed

and the number of molecules. i explained it in my last e-mail.

however, compute temp/region does care about molecules and the extra

parameter is for *total* degrees of freedom to be removed. since 1/3rd of

the DOFs is removed, why don't you just multiple the result by 1.5 and

be happy? think about this for a bit, look at the formula in the documentation

and pick up a statistical mechanics text book and re-read the part about

the relation between macroscopic properties like temperature and statistical

mechanical ensembles. ...and wait for the spark.

axel.