Action: SHADOW

Module	isdb
Description	Usage
Communicate atoms positions among replicas and calculate the RMSD with respect to a mother (reference) simulation.
output value	type
the value of the shadow RMSD	scalar

Details and examples

Communicate atoms positions among replicas and calculate the RMSD with respect to a mother (reference) simulation.

The option UPDATE allows to specify the stride for communication between mother and replica systems. The flag REFERENCE needs to be specified in the input file of the mother replica. This action must be run in a multi-replica framework (such as the -multi option in GROMACS).

Examples

In this example, we perform a simulation of a RNA molecule using two replicas: a mother and a shadow replica. The mother simulation communicates the coordinates of the RNA backbone to the replica every 100 steps. The RMSD of the replica with respect to the mother is calculated on the RNA backbone atoms and an UPPER_WALLS is applied at 0.2 nm. The mother replica contains also the UPPER_WALLS action. However, the forces on the RNA atoms of the mother replica are automatically set to zero inside the SHADOW action.

The input file for the mother simulation looks as follows:

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

# Reference PDB
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=conf_emin_PLUMED.pdb WHOLE The reference structure is whole, i
# Define RNA nucleic backbone
The MOLINFO action with label  calculates somethingrna: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1,2,5,6,33,36,37,40,41,67,70,71,74,75,98,101,102,105,106,131,134,135,138,139,165,168,169,172,173,198,201,202,205,206,228,231,232,235,236,259,262,263,266,267,289,292,293,296,297,323,326,327,330,331,356,359,360,363,364,390,393,394,397,398,421,424,425,428,429,452,455,456,459,460,482,485,486,489,490,516,519,520,523,524,550,553,554,557,558,584,587,588,591,592,617,620,621,624,625,651,654,655,658,659,682,685,686,689,690,712,715,716,719,720,743,746,747,750,751,773,776,777,780,781,804,807,808,811,812,834,837,838,841,842,868,871,872,875,876,899,902,903,906,907
# Reconstruct RNA PBC
The GROUP action with label rna calculates somethingWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=rna EMST only for backward compatibility, as of PLUMED 2 STRIDE the frequency with which molecules are reassembled=1

# Define shadow RMSD on RNA backbone
rmsd: SHADOWCommunicate atoms positions among replicas and calculate the RMSD with respect to a mother (reference) simulation. More details ATOMSatoms for which we calculate the shadow RMSD=rna NOPBC ignore the periodic boundary conditions when calculating distances UPDATEstride for updating reference coordinates=100 REFERENCE this is the reference replica
# Add upper wall - derivatives are set to zero inside SHADOW action
The SHADOW action with label rmsd calculates the following quantities:
 Quantity   
 Description  
rmsd.value
the value of the shadow RMSDuws: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rmsd ATthe positions of the wall=0.2 KAPPAthe force constant for the wall=10000.0 STRIDEthe frequency with which the forces due to the bias should be calculated=1

# Print useful info
The UPPER_WALLS action with label uws calculates the following quantities:
 Quantity   
 Description  
uws.bias
the instantaneous value of the bias potential
uws.force2
the instantaneous value of the squared force due to this bias potentialPRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=500 ARGthe labels of the values that you would like to print to the file=rmsd,uws.bias

while the input file for a shadow replica looks like:

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

# Reference PDB
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=conf_emin_PLUMED.pdb WHOLE The reference structure is whole, i
# Define RNA nucleic backbone
The MOLINFO action with label  calculates somethingrna: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1,2,5,6,33,36,37,40,41,67,70,71,74,75,98,101,102,105,106,131,134,135,138,139,165,168,169,172,173,198,201,202,205,206,228,231,232,235,236,259,262,263,266,267,289,292,293,296,297,323,326,327,330,331,356,359,360,363,364,390,393,394,397,398,421,424,425,428,429,452,455,456,459,460,482,485,486,489,490,516,519,520,523,524,550,553,554,557,558,584,587,588,591,592,617,620,621,624,625,651,654,655,658,659,682,685,686,689,690,712,715,716,719,720,743,746,747,750,751,773,776,777,780,781,804,807,808,811,812,834,837,838,841,842,868,871,872,875,876,899,902,903,906,907
# Reconstruct RNA PBC
The GROUP action with label rna calculates somethingWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=rna EMST only for backward compatibility, as of PLUMED 2 STRIDE the frequency with which molecules are reassembled=1

# Define shadow RMSD on RNA backbone
rmsd: SHADOWCommunicate atoms positions among replicas and calculate the RMSD with respect to a mother (reference) simulation. More details ATOMSatoms for which we calculate the shadow RMSD=rna NOPBC ignore the periodic boundary conditions when calculating distances UPDATEstride for updating reference coordinates=100
# Add upper wall
The SHADOW action with label rmsd calculates the following quantities:
 Quantity   
 Description  
rmsd.value
the value of the shadow RMSDuws: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rmsd ATthe positions of the wall=0.2 KAPPAthe force constant for the wall=10000.0 STRIDEthe frequency with which the forces due to the bias should be calculated=1

# Print useful info
The UPPER_WALLS action with label uws calculates the following quantities:
 Quantity   
 Description  
uws.bias
the instantaneous value of the bias potential
uws.force2
the instantaneous value of the squared force due to this bias potentialPRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=500 ARGthe labels of the values that you would like to print to the file=rmsd,uws.bias

Input

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

Keyword	Type	Description
ATOMS	atoms	atoms for which we calculate the shadow RMSD

Full list of keywords

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

Keyword	Type	Default	Description
ATOMS	input	none	atoms for which we calculate the shadow RMSD
UPDATE	compulsory	none	stride for updating reference coordinates
NUMERICAL_DERIVATIVESThis keyword do not have examples	optional	false	calculate the derivatives for these quantities numerically
NOPBC	optional	false	ignore the periodic boundary conditions when calculating distances
REFERENCE	optional	false	this is the reference replica