[gmx-users] About Temperature Calculation

David spoel at xray.bmc.uu.se
Thu Apr 1 16:46:01 CEST 2004

On Fri, 2004-04-02 at 16:19, Ane Xu wrote:

>      So, the 0K equilibrium potential (what I got from "em") is not the
> "quilibrium" one in the 300K or 500K case, and if I wanna got a system
> at 300K, the only way is to do "SD" or "MD" with higher initial
> temperature (which results in a equilibrium 300K state). Is it right?
> >just a NVE simulation with
> >gen_temp=300.
> in your file you have gen_temp = 500  !!! That explains why you have a 
> initial
> temperature of 500 K

It could be that grompp estimates the number of degrees of freedom
incorrectly. Please check the number. If you have a CNT in principle
every carbon has three bonds.  If you use constraints that will mean
that each carbon has 1.5 (3 - 3*0.5) degrees of freedom. If you do not
use constraints it should simply be 3 per carbon.

>     I test a case of 500K (which results in 250K finally) after 300K, I
> forgot to explain, I am sorry for that.
>     Thanks.
> Ane
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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