Action: ABMD

Module	bias
Description	Usage
Adds a ratchet-and-pawl like restraint on one or more variables.

Output components

This action calculates the values in the following table. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.

Input

The arguments that serve as the input for this action are specified using one or more of the keywords in the following table.

Further details and examples

Adds a ratchet-and-pawl like restraint on one or more variables.

This action can be used to evolve a system towards a target value in CV space using an harmonic potential that moves with the thermal fluctuations of the CV. This method was introduced in the papers cited below. In it the biasing potential in this method is as follows:

$$V(\rho(t)) = \left \{ \begin{array}{ll} \frac{K}{2}\left(\rho(t)-\rho_m(t)\right)^2, &\rho(t)>\rho_m(t)\\ 0, & \rho(t)\le\rho_m(t), \end{array} \right .$$

where

$$\rho(t)=\left(CV(t)-TO\right)^2$$

and

$$\rho_m(t)=\min_{0\le\tau\le t}\rho(\tau)+\eta(t)$$ .

The method is based on the introduction of a biasing potential which is zero when the system is moving towards the desired arrival point and which damps the fluctuations when the system attempts to move in the opposite direction. As in the case of the ratchet and pawl system, propelled by thermal motion of the solvent molecules, the biasing potential does not exert work on the system. $\eta(t)$ is an additional white noise acting on the minimum position of the bias.

Examples

The following input sets up two biases, one on the distance between atoms 3 and 5 and another on the distance between atoms 2 and 4. The two target values are defined using TO and the two strength using KAPPA. The total energy of the bias is printed.

Click on the labels of the actions for more information on what each action computes

DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3,5 LABELa label for the action so that its output can be referenced in the input to other actions=d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1
scalar
the DISTANCE between this pair of atoms
DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,4 LABELa label for the action so that its output can be referenced in the input to other actions=d2The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2
scalar
the DISTANCE between this pair of atoms
ABMDAdds a ratchet-and-pawl like restraint on one or more variables. More details ARGthe labels of the scalars on which the bias will act=d1,d2 TOThe array of target values=1.0,1.5 KAPPAThe array of force constants=5.0,5.0 LABELa label for the action so that its output can be referenced in the input to other actions=abmdThe ABMD action with label abmd calculates the following quantities:
 Quantity   
 Type   
 Description  
abmd.bias
scalar
the instantaneous value of the bias potential
abmd.d1_min
scalar
one or multiple instances of this quantity can be referenced elsewhere in the input file.  These quantities will be named with the arguments of the bias followed by the character string _min. These quantities tell the user the minimum value assumed by rho_m(t). This particular component measures this quantity for the input CV named d1
abmd.d2_min
scalar
one or multiple instances of this quantity can be referenced elsewhere in the input file.  These quantities will be named with the arguments of the bias followed by the character string _min. These quantities tell the user the minimum value assumed by rho_m(t). This particular component measures this quantity for the input CV named d2
abmd.force2
scalar
the instantaneous value of the squared force due to this bias potential
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=abmd.bias,abmd.d1_min,abmd.d2_min

References

More information about how this action can be used is available in the following articles:

• M. Marchi, P. Ballone, Adiabatic bias molecular dynamics: A method to navigate the conformational space of complex molecular systems. The Journal of Chemical Physics. 110, 3697–3702 (1999)
• D. Provasi, M. Filizola, Putative Active States of a Prototypic G-Protein-Coupled Receptor from Biased Molecular Dynamics. Biophysical Journal. 98, 2347–2355 (2010)
• C. Camilloni, R. A. Broglia, G. Tiana, Hierarchy of folding and unfolding events of protein G, CI2, and ACBP from explicit-solvent simulations. The Journal of Chemical Physics. 134 (2011)

Syntax

The following table describes the keywords and options that can be used with this action