[gmx-users] number of degrees of freedom
Carmen Domene
carmen.domene at bioch.ox.ac.uk
Thu Nov 7 17:02:59 CET 2002
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.
In the case of water molecules, I should get 47628 instead of 47626.23 for
example.
I need to know the number of degrees of freedom because I would like to
calculate the temperature for each of the species of this system (that
is the temperature of the Protein, the temperature of the K etc.) when I
couple in the way:
; Groups to couple separately =
tc-grps = PROTEIN_K POPC SOL_CL
with
Number of degrees of freedom in T-Coupling group PROTEIN_K is 7748.71
Number of degrees of freedom in T-Coupling group POPC is 25409.06
Number of degrees of freedom in T-Coupling group SOL_Cl is 47671.23
Thanks, Carmen
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