SHADOW
This is part of the isdb module

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
tested on master
# Reference PDB
MOLINFO 
STRUCTURE
compulsory keyword 
a file in pdb format containing a reference structure. 
=conf_emin_PLUMED.pdb 
WHOLE
( default=off ) The reference structure is whole, i.e. 
 
# Define RNA nucleic backbone
rna: GROUP 
ATOMS
the 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
WHOLEMOLECULES 
ENTITY0
the atoms that make up a molecule that you wish to align. 
=rna 
EMST
( default=off ) Define atoms sequence in entities using an Euclidean minimum spanning
tree 
 
STRIDE
compulsory keyword ( default=1 )
the frequency with which molecules are reassembled. 
=1 
# Define shadow RMSD on RNA backbone
rmsd: SHADOW 
ATOMS
atoms for which we calculate the shadow RMSD. 
=rna 
NOPBC
( default=off ) ignore the periodic boundary conditions when calculating distances

 
UPDATE
compulsory keyword 
stride for updating reference coordinates 
=100 
REFERENCE
( default=off ) this is the reference replica 
 
# Add upper wall - derivatives are set to zero inside SHADOW action
uws: UPPER_WALLS 
ARG
the arguments on which the bias is acting. 
=rmsd 
AT
compulsory keyword 
the positions of the wall. 
=0.2 
KAPPA
compulsory keyword 
the force constant for the wall. 
=10000.0 
STRIDE
the frequency with which the forces due to the bias should be calculated. 
=1 
# Print useful info
PRINT 
FILE
the name of the file on which to output these quantities 
=COLVAR 
STRIDE
compulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output 
=500 
ARG
compulsory keyword 
the 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
tested on master
# Reference PDB
MOLINFO 
STRUCTURE
compulsory keyword 
a file in pdb format containing a reference structure. 
=conf_emin_PLUMED.pdb 
WHOLE
( default=off ) The reference structure is whole, i.e. 
 
# Define RNA nucleic backbone
rna: GROUP 
ATOMS
the 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
WHOLEMOLECULES 
ENTITY0
the atoms that make up a molecule that you wish to align. 
=rna 
EMST
( default=off ) Define atoms sequence in entities using an Euclidean minimum spanning
tree 
 
STRIDE
compulsory keyword ( default=1 )
the frequency with which molecules are reassembled. 
=1 
# Define shadow RMSD on RNA backbone
rmsd: SHADOW 
ATOMS
atoms for which we calculate the shadow RMSD. 
=rna 
NOPBC
( default=off ) ignore the periodic boundary conditions when calculating distances

 
UPDATE
compulsory keyword 
stride for updating reference coordinates 
=100 
# Add upper wall
uws: UPPER_WALLS 
ARG
the arguments on which the bias is acting. 
=rmsd 
AT
compulsory keyword 
the positions of the wall. 
=0.2 
KAPPA
compulsory keyword 
the force constant for the wall. 
=10000.0 
STRIDE
the frequency with which the forces due to the bias should be calculated. 
=1 
# Print useful info
PRINT 
FILE
the name of the file on which to output these quantities 
=COLVAR 
STRIDE
compulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output 
=500 
ARG
compulsory keyword 
the labels of the values that you would like to print to the file 
=rmsd,uws.bias
Glossary of keywords and components
Description of components

By default the value of the calculated quantity can be referenced elsewhere in the input file by using the label of the action. Alternatively this Action can be used to calculate the following quantities by employing the keywords listed below. These quantities can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.

Quantity Description
.#!value the value of the shadow RMSD
The atoms involved can be specified using
ATOMS atoms for which we calculate the shadow RMSD. For more information on how to specify lists of atoms see Groups and Virtual Atoms
Compulsory keywords
UPDATE stride for updating reference coordinates
Options
NUMERICAL_DERIVATIVES ( default=off ) calculate the derivatives for these quantities numerically
NOPBC ( default=off ) ignore the periodic boundary conditions when calculating distances
REFERENCE

( default=off ) this is the reference replica