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The AFM Module of CHARMM

By Emanuele Paci, 1997/2000

AFM is an external perturbation designed to pull macromolecules mimicking single molecule experiments (AFM or LOT). There are three possible way of simulating the pulling; all consist in applying a suitable force to two atoms. The force is identical in magnitude for the two atoms, parallel to the two atoms and directed in the direction of increasing distance. The difference in the forces applied concerns their dependence on the time. The three methods currently implemented are:

  1. constant force.
  2. steered molecular dynamics
  3. biased molecular dynamics (see HQBM.DOC)

References:

  1. Paci & Karplus, PNAS, 97, 6521-6526, (2000),
  2. Paci et al., JMB, 314, 589-605, (2001).

Syntax

[INPUT AFM command]

  AFM  METHOD ALPHA real [BETA real] two-atom-selection -
             [IUNJ integer] [XIMAX real]

  AFM RESEt
METHOD one of CF, BMD, SMD
ALPHA force constant (in pN (CF) or pN/Å (SMD/BMD))
BETA cantilever speed (in Å/ps only for SMD)
IUNJ

write the output

 istep rc[Å] rc_ref[Å] force[pN] energy[kcal/mol]

on unit IUNJ
XIMAX stops the run when the distance between the two selected atoms exceeds XIMAX
RESEt resets the logicals and turns off the afm module.