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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