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!
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
