Action: RANDOM_EXCHANGES

Module	generic
Description	Usage
Set random pattern for exchanges.

Further details and examples

Set random pattern for exchanges.

This command is typically used if you are using the bias exchange method that is discussed in the paper in the bibliography. When it is present it tells PLUMED not do do exchanges between replicas with consecutive indices and instad to use use a random pattern.

The following three example input files show how one can run a bias exchange metadynamics simulation using a different angle in each replica. Exchanges are randomly tried between replicas 0-1, 0-2 and 1-2

Here is plumed.0.dat

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

RANDOM_EXCHANGESSet random pattern for exchanges. More details
The RANDOM_EXCHANGES action with label  calculates somethingtThe TORSION action with label t calculates the following quantities:
 Quantity   
 Type   
 Description  
t
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=1,2,3,4
METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=t HEIGHTthe heights of the Gaussian hills=0.1 PACEthe frequency for hill addition=100 SIGMAthe widths of the Gaussian hills=0.3

Here is plumed.1.dat

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

RANDOM_EXCHANGESSet random pattern for exchanges. More details
The RANDOM_EXCHANGES action with label  calculates somethingtThe TORSION action with label t calculates the following quantities:
 Quantity   
 Type   
 Description  
t
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=2,3,4,5
METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=t HEIGHTthe heights of the Gaussian hills=0.1 PACEthe frequency for hill addition=100 SIGMAthe widths of the Gaussian hills=0.3

Here is plumed.2.dat

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

RANDOM_EXCHANGESSet random pattern for exchanges. More details
The RANDOM_EXCHANGES action with label  calculates somethingtThe TORSION action with label t calculates the following quantities:
 Quantity   
 Type   
 Description  
t
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=3,4,5,6
METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=t HEIGHTthe heights of the Gaussian hills=0.1 PACEthe frequency for hill addition=100 SIGMAthe widths of the Gaussian hills=0.3

Notice that you can perform the same calculation with the following single PLUMED input file:

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

#SETTINGS NREPLICAS=3

RANDOM_EXCHANGESSet random pattern for exchanges. More details
The RANDOM_EXCHANGES action with label  calculates somethingt1The TORSION action with label t1 calculates the following quantities:
 Quantity   
 Type   
 Description  
t1
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=1,2,3,4
t2The TORSION action with label t2 calculates the following quantities:
 Quantity   
 Type   
 Description  
t2
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=2,3,4,5
t3The TORSION action with label t3 calculates the following quantities:
 Quantity   
 Type   
 Description  
t3
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=3,4,5,6
METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=@replicas:This keyword specifies that different replicas have different values for this quantity.  See here for more details.t1,t2,t3 HEIGHTthe heights of the Gaussian hills=0.1 PACEthe frequency for hill addition=100 SIGMAthe widths of the Gaussian hills=0.3

[!CAUTION] Multi replica simulations are presently only working with gromacs.

[!CAUTION] The directive should appear in the input file for every replica. If SEED is specified, it should be the same in all input files.

References

More information about how this action can be used is available in the following articles: - S. Piana, A. Laio, A Bias-Exchange Approach to Protein Folding. The Journal of Physical Chemistry B. 111, 4553–4559 (2007)

Syntax

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