[gmx-users] Calculating Temperature from Velocity

[Andy Shelley]

Jochen,

I am confused on how to calculate the bond length constraints.  I notice
after I run grompp it gives the output of degrees of freedom:

Number of degrees of freedom in T-Coupling group TOP is 59.97
Number of degrees of freedom in T-Coupling group BOTTOM is 59.97
Number of degrees of freedom in T-Coupling group NIT is 9355.37
Number of degrees of freedom in T-Coupling group OXY is 2638.69
Number of degrees of freedom in T-Coupling group UNK is 5874.00

In the TOP and BOTTOM group I have 20 atoms. 3120 atoms in NIT, 880 atoms in
OXY and 1960 atoms in UNK. I not sure how these numbers were calculated. If
I add up all the degrees of freedom then it is 3N-12. I know N_com =3
because the center of mass velocities of constant of motion, so does LINCS
account for the other 9?

Thanks,
Andy
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