Dear all,<br>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:<br><br>Initializing pull groups. Inv. mass of group 1: 0.024950<br>Initial coordinates center of mass: 3.966 3.338 3.648<br>Initializing reference group. Inv. mass: 0.000132<br>Initial coordinates center of mass: 3.162 3.127 3.097<br>Initial distance of group 1: 0.998<br><br>Pull rate: 5.000000e-01 nm/ns. Force constant: 1.000000e+03 kJ/(mol nm)<br>Pull direction: 0.806 0.212 0.552<br><br>what makes these different?<br><br>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"??<br><br>Could anybody here tell me why? I am crazy about these problem! <br><!-- urlfiles --><br><br><!-- footer --><br><br>
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