[gmx-users] zero temperature II

Berk Hess gmx3 at hotmail.com
Mon Apr 5 10:31:01 CEST 2004

>dear all,
>In a previous mail I mentioned a problem
>with zero temperature output. I seem to have found what the problem is and 
>this looks like
>a bug, or at least an undocumented limitation.
>When I do md with a system containing only frozen atoms and (not-frozen) 
>water both ener.edr and md.log say that the kinetic energy and the 
>temperature are
>zero. The thermostate seems to work though, because
>my system does not "explode".
>If I "un-freeze" the frozen atoms the
>output is back to normal. The fact that frozen atoms
>are formally provided with an infinite mass
>might somehow cause this problem.
>Any ideas for a work-around ?
>Where in the code is E_kin calculated ?

I have tested this some time ago (but I don't remember if I mailed it to the 
and for me it works fine. Both with berendsen and nose-hoover coupling
I get Ekin and temperatures that are normal.
I don't know which features of your system might cause the problem.

Frozen atoms are not formally provided with an infinite mass.
Very large masses are only used in the constraint algorithms to
treat constaints between frozen and non-frozen particles.


MSN Search, for accurate results! http://search.msn.nl

More information about the gromacs.org_gmx-users mailing list