[gmx-users] Problem in AFM pulling, the parameter unit and direction definition!

clark clarkzhy at tom.com
Sat Nov 25 04:24:29 CET 2006

Dear all,
I am confused about the unit of some parameters in AFM pulling function. In manual 3.3, page 117, the unit of "afm_rate" is nm/ps, and unit of afm_k is kJ mol-1 nm-2. But in the output file(*.log), there is another unit:

Initializing pull groups. Inv. mass of group 1: 0.024950
Initial coordinates center of mass:    3.966    3.338    3.648
Initializing reference group. Inv. mass: 0.000132
Initial coordinates center of mass:    3.162    3.127    3.097
Initial distance of group 1:    0.998

Pull rate: 5.000000e-01 nm/ns. Force constant: 1.000000e+03 kJ/(mol nm)
Pull direction:    0.806    0.212    0.552

what makes these different?

and "Pull direction" seems to be gotten by subtracting coordinates of referencePgroup from coordinates of pull group. This value of "Pull direction:    0.806    0.212    0.552" is different from what I set in pull.ppa files,which is "afm_dir1	= 0.588 0.428 -0.686"??

Could anybody here tell me why? I am crazy about these problem! 

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