[gmx-users] number of degrees of freedom

[David van der Spoel]

On Thu, 2002-11-07 at 17:02, Carmen Domene wrote:
> 
> Dear all,
> 
> I am running a simulation which has:
> 
> ; Compound        #mols
> PROTEIN              4
> POPC               242
> SOL               7938
> CL                  15
> K                    3
> 
> After running grompp, I get the following output:
> 
> Number of degrees of freedom in T-Coupling group Protein is 7739.71
> Number of degrees of freedom in T-Coupling group POPC is 25409.06
> Number of degrees of freedom in T-Coupling group SOL is 47626.23
> Number of degrees of freedom in T-Coupling group Cl is 45.00
> Number of degrees of freedom in T-Coupling group K is 9.00
> 
> I was wondering why I do not get integer numbers for the protein, the
> lipid and the water molecules.
I think it is somewhere in the manual. We subtract three degrees of
freedom for overall translation, and these are evenly spread over all
the groups.


-- 
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://xray.bmc.uu.se/~spoel
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