afm (c41b1)
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 | Syntax of the AFM command
* Function | Purpose of each of the keywords
* Input | AFM Input Description
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 | Syntax of the AFM command
* Function | Purpose of each of the keywords
* Input | AFM Input Description
Top
[INPUT AFM command]
AFM METHOD ALPHA real [BETA real] two-atom-selection -
[IUNJ integer] [XIMAX real]
AFM RESEt
[INPUT AFM command]
AFM METHOD ALPHA real [BETA real] two-atom-selection -
[IUNJ integer] [XIMAX real]
AFM RESEt
Top
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.
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.