[gmx-users] temperature too low

w.j.schravendijk at students.pharm.uu.nl w.j.schravendijk at students.pharm.uu.nl
Tue Feb 26 14:56:26 CET 2002

Thank you!

Temperatures mentioned in the md.log file are around 3.0 10^2 K, as

   nrdf:             521.971       53943

8991 water molecules are present. Assuming 6 degrees of freedom (I used
rigid water) will result in a total of 53946 degrees of freedom, which
correlates with the second number. The first should have to do something
with my protein, but I cannot exactly figure out how.

It seems that the simulation has run correctly, but that g_traj generates
the wrong output. Is there any way I could fix this? Are there other
g_** programs that are vulnerable for the value of the degrees of freedom?

BTW: (I've checked cut-off as well as PME and gen forcefield, it all
resulted in the 2/3 temperature output from g_traj)

Greetings, Pim

On Tue, 26 Feb 2002, David van der Spoel wrote:

> Since your temperature is exactly two/thirds of what it should be, it
> could be that you have a problem with the number of degrees of freedom.
> Please check whether it is 6 or 9 per molecule (it's printed in md.log for
> the total system). You have 6 degrees of freedom for a rigid water, 9 for
> a flexible.
> Otherwise try to change the reaction0field into a cut-off and retry.
> --
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
> Husargatan 3, Box 576,  	75123 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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