CHARMM c32b1 afm.doc

File: Afm ]-[ Node: Top
Up: (commands.doc) -=- Next: Syntax\n

                       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).
 
* Menu:

* Syntax::              Syntax of the AFM command
* Function::            Purpose of each of the keywords
* Input::               AFM Input Description

File: Afm ]-[ Node: Syntax
Up: Top -=- Previous: Top -=- Next: Function\n

[INPUT AFM command]

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

  AFM RESEt

File: Afm ]-[ Node: Function
Previous: Syntax -=- Up: Top -=- Next: Top\n

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.

CHARMM .doc Homepage

Information and HTML Formatting Courtesy of:

NIH/DCRT/Laboratory for Structural Biology
FDA/CBER/OVRR Biophysics Laboratory
Modified, updated and generalized by C.L. Brooks, III
The Scripps Research Institute