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| 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).
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:
# Reference PDB MOLINFO STRUCTUREcompulsory 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 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 WHOLEMOLECULES ENTITY0the 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 STRIDEcompulsory keyword ( default=1 ) the frequency with which molecules are reassembled. =1 # Define shadow RMSD on RNA backbone rmsd: SHADOW ATOMSatoms for which we calculate the shadow RMSD. =rna NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances UPDATEcompulsory 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 ARGthe arguments on which the bias is acting. =rmsd ATcompulsory keyword the positions of the wall. =0.2 KAPPAcompulsory keyword the force constant for the wall. =10000.0 STRIDEthe frequency with which the forces due to the bias should be calculated. =1 # Print useful info PRINT FILEthe name of the file on which to output these quantities =COLVAR STRIDEcompulsory keyword ( default=1 ) the frequency with which the quantities of interest should be output =500 ARGthe input for this action is the scalar output from one or more other actions. =rmsd,uws.bias
while the input file for a shadow replica looks like:
# Reference PDB MOLINFO STRUCTUREcompulsory 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 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 WHOLEMOLECULES ENTITY0the 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 STRIDEcompulsory keyword ( default=1 ) the frequency with which molecules are reassembled. =1 # Define shadow RMSD on RNA backbone rmsd: SHADOW ATOMSatoms for which we calculate the shadow RMSD. =rna NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances UPDATEcompulsory keyword stride for updating reference coordinates =100 # Add upper wall uws: UPPER_WALLS ARGthe arguments on which the bias is acting. =rmsd ATcompulsory keyword the positions of the wall. =0.2 KAPPAcompulsory keyword the force constant for the wall. =10000.0 STRIDEthe frequency with which the forces due to the bias should be calculated. =1 # Print useful info PRINT FILEthe name of the file on which to output these quantities =COLVAR STRIDEcompulsory keyword ( default=1 ) the frequency with which the quantities of interest should be output =500 ARGthe input for this action is the scalar output from one or more other actions. =rmsd,uws.bias
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 |
| ATOMS | atoms for which we calculate the shadow RMSD. For more information on how to specify lists of atoms see Groups and Virtual Atoms |
| UPDATE | stride for updating reference coordinates |
| 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 |
1.13.2