PLUMED-NEST-TEST-SITE

Project ID: plumID:24.016
Source: 2-ss-refinement/plumed_EMMI.dat
Originally used with PLUMED version: 2.9
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

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

# if you are restarting the run, please uncomment this line
#RESTART
# include topology info
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=../top/ref.pdb  WHOLE The reference structure is whole, i

# define map atoms
The MOLINFO action with label  calculates somethingsystem-mapThe GROUP action with label system-map calculates the following quantities:
 Quantity   
 Type   
 Description  
system-map
atoms
indices of atoms specified in GROUP: 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 NDX_FILEthe name of index file (gromacs syntax)=../top/index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=System-MAP

# make map atoms whole 
WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ...
ADDREFERENCE Define the reference position of the first atom of each entity using a PDB file EMST only for backward compatibility, as of PLUMED 2
ENTITY0the atoms that make up a molecule that you wish to align=system-map STRIDE the frequency with which molecules are reassembled=4
... WHOLEMOLECULES

# create EMMI score
EMMIVOXBayesian single-structure and ensemble refinement with cryo-EM maps. More details ...
# name of this action
LABELa label for the action so that its output can be referenced in the input to other actions=emmiThe EMMIVOX action with label emmi calculates the following quantities:
 Quantity   
 Type   
 Description  
emmi.scoreb
scalar
Bayesian score
emmi.scale
scalar
scale factor
emmi.offset
scalar
offset
emmi.kbt
scalar
temperature in energy unit
emmi.accB
scalar
Bfactor MC acceptance
emmi.corr
scalar
correlation coefficient
# general parameters - do not change this!
# NL_STRIDE: update neighbor list stride
# NL_DIST_CUTOFF: distance cutoff in nm
# NL_GAUSS_CUTOFF: cutoff based on the Gaussian sigma
TEMPtemperature=300.0 NL_STRIDEneighbor list update frequency=50 NL_DIST_CUTOFFneighbor list distance cutoff=1.0 NL_GAUSS_CUTOFFneighbor list Gaussian sigma cutoff=3.0
# define atoms for cryo-EM restraint and read experimental data
ATOMSatoms used in the calculation of the density map, typically all heavy atoms=system-map DATA_FILEfile with cryo-EM map=emd_plumed_aligned.dat
# info about the experimental map
NORM_DENSITYintegral of experimental density=6846.255371 RESOLUTIONcryo-EM map resolution=0.36
# data likelihood (or noise model): Marginal
SIGMA_MINminimum density error=0.2 GPU calculate EMMIVOX on GPU with Libtorch
# output: in production write with the frequency at which XTC/TRR are written
STATUS_FILEwrite a file with all the data useful for restart=EMMIStatus WRITE_STRIDEstride for writing status file=5000
# comment this if you have a hetero-complex
#BFACT_NOCHAIN
# in production, you should sample Bfactors
DBFACTBfactor MC step=0.05 MCBFACT_STRIDEBfactor MC stride=500 BFACT_SIGMABfactor sigma prior=0.1
# scale factor
SCALEscale factor=1.250000
# correlation
CORRELATION calculate correlation coefficient
...

# in production, apply bias to system
# translate into bias - updated every 2/4 time steps
# emr: BIASVALUE ARG=emmi.scoreb STRIDE=2
emrThe BIASVALUE action with label emr calculates the following quantities:
 Quantity   
 Type   
 Description  
emr.bias
scalar
the instantaneous value of the bias potential
emr.emmi.scoreb_bias
scalar
one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with  the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named emmi.scoreb: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=emmi.scoreb STRIDEthe frequency with which the forces due to the bias should be calculated=4
#
# print output to file
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=emmi.* FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=5000


eRMSD1The ERMSD action with label eRMSD1 calculates the following quantities:
 Quantity   
 Type   
 Description  
eRMSD1
scalar
the eRMSD between the instantaneous structure and the reference structure that was input: ERMSDCalculate eRMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../helix-templates/UAGC_36-39_c246_o.pdb ATOMSthe list of atoms (use lcs)=@lcs-36an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 36. Click here for more information. ,@lcs-37an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 37. Click here for more information. ,@lcs-38an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 38. Click here for more information. ,@lcs-39an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 39. Click here for more information. ,@lcs-47an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 47. Click here for more information. ,@lcs-48an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 48. Click here for more information. ,@lcs-49an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 49. Click here for more information. ,@lcs-50an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 50. Click here for more information. 
eRMSD1: ERMSDCalculate eRMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../helix-templates/UAGC_36-39_c246_o.pdb ATOMSthe list of atoms (use lcs)=@lcs-36an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 36. Click here for more information. ,@lcs-37an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 37. Click here for more information. ,@lcs-38an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 38. Click here for more information. ,@lcs-39an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 39. Click here for more information. ,@lcs-47an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 47. Click here for more information. ,@lcs-48an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 48. Click here for more information. ,@lcs-49an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 49. Click here for more information. ,@lcs-50an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 50. Click here for more information.   CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=2.4
eRMSD2The ERMSD action with label eRMSD2 calculates the following quantities:
 Quantity   
 Type   
 Description  
eRMSD2
scalar
the eRMSD between the instantaneous structure and the reference structure that was input: ERMSDCalculate eRMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../helix-templates/GGA_530-532_c246_o.pdb ATOMSthe list of atoms (use lcs)=@lcs-530an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 530. Click here for more information. ,@lcs-531an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 531. Click here for more information. ,@lcs-532an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 532. Click here for more information. ,@lcs-538an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 538. Click here for more information. ,@lcs-539an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 539. Click here for more information. ,@lcs-540an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 540. Click here for more information. 
eRMSD2: ERMSDCalculate eRMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../helix-templates/GGA_530-532_c246_o.pdb ATOMSthe list of atoms (use lcs)=@lcs-530an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 530. Click here for more information. ,@lcs-531an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 531. Click here for more information. ,@lcs-532an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 532. Click here for more information. ,@lcs-538an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 538. Click here for more information. ,@lcs-539an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 539. Click here for more information. ,@lcs-540an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 540. Click here for more information.   CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=2.4
eRMSD3The ERMSD action with label eRMSD3 calculates the following quantities:
 Quantity   
 Type   
 Description  
eRMSD3
scalar
the eRMSD between the instantaneous structure and the reference structure that was input: ERMSDCalculate eRMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../helix-templates/ACC_664-666_c246_o.pdb ATOMSthe list of atoms (use lcs)=@lcs-664an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 664. Click here for more information. ,@lcs-665an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 665. Click here for more information. ,@lcs-666an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 666. Click here for more information. ,@lcs-716an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 716. Click here for more information. ,@lcs-717an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 717. Click here for more information. ,@lcs-718an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 718. Click here for more information. 
eRMSD3: ERMSDCalculate eRMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../helix-templates/ACC_664-666_c246_o.pdb ATOMSthe list of atoms (use lcs)=@lcs-664an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 664. Click here for more information. ,@lcs-665an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 665. Click here for more information. ,@lcs-666an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 666. Click here for more information. ,@lcs-716an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 716. Click here for more information. ,@lcs-717an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 717. Click here for more information. ,@lcs-718an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 718. Click here for more information.   CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=2.4
eRMSD4The ERMSD action with label eRMSD4 calculates the following quantities:
 Quantity   
 Type   
 Description  
eRMSD4
scalar
the eRMSD between the instantaneous structure and the reference structure that was input: ERMSDCalculate eRMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../helix-templates/ACGG_669-672_c246_o.pdb ATOMSthe list of atoms (use lcs)=@lcs-669an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 669. Click here for more information. ,@lcs-670an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 670. Click here for more information. ,@lcs-671an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 671. Click here for more information. ,@lcs-672an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 672. Click here for more information. ,@lcs-710an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 710. Click here for more information. ,@lcs-711an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 711. Click here for more information. ,@lcs-712an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 712. Click here for more information. ,@lcs-713an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 713. Click here for more information. 
eRMSD4: ERMSDCalculate eRMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../helix-templates/ACGG_669-672_c246_o.pdb ATOMSthe list of atoms (use lcs)=@lcs-669an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 669. Click here for more information. ,@lcs-670an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 670. Click here for more information. ,@lcs-671an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 671. Click here for more information. ,@lcs-672an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 672. Click here for more information. ,@lcs-710an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 710. Click here for more information. ,@lcs-711an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 711. Click here for more information. ,@lcs-712an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 712. Click here for more information. ,@lcs-713an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 713. Click here for more information.   CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=2.4
eRMSD5The ERMSD action with label eRMSD5 calculates the following quantities:
 Quantity   
 Type   
 Description  
eRMSD5
scalar
the eRMSD between the instantaneous structure and the reference structure that was input: ERMSDCalculate eRMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../helix-templates/GCU_679-681_c246_o.pdb ATOMSthe list of atoms (use lcs)=@lcs-679an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 679. Click here for more information. ,@lcs-680an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 680. Click here for more information. ,@lcs-681an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 681. Click here for more information. ,@lcs-704an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 704. Click here for more information. ,@lcs-705an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 705. Click here for more information. ,@lcs-706an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 706. Click here for more information. 
eRMSD5: ERMSDCalculate eRMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../helix-templates/GCU_679-681_c246_o.pdb ATOMSthe list of atoms (use lcs)=@lcs-679an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 679. Click here for more information. ,@lcs-680an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 680. Click here for more information. ,@lcs-681an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 681. Click here for more information. ,@lcs-704an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 704. Click here for more information. ,@lcs-705an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 705. Click here for more information. ,@lcs-706an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 706. Click here for more information.   CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=2.4
eRMSD6The ERMSD action with label eRMSD6 calculates the following quantities:
 Quantity   
 Type   
 Description  
eRMSD6
scalar
the eRMSD between the instantaneous structure and the reference structure that was input: ERMSDCalculate eRMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../helix-templates/GGC_682-684_c246_o.pdb ATOMSthe list of atoms (use lcs)=@lcs-682an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 682. Click here for more information. ,@lcs-683an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 683. Click here for more information. ,@lcs-684an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 684. Click here for more information. ,@lcs-699an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 699. Click here for more information. ,@lcs-700an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 700. Click here for more information. ,@lcs-701an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 701. Click here for more information. 
eRMSD6: ERMSDCalculate eRMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../helix-templates/GGC_682-684_c246_o.pdb ATOMSthe list of atoms (use lcs)=@lcs-682an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 682. Click here for more information. ,@lcs-683an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 683. Click here for more information. ,@lcs-684an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 684. Click here for more information. ,@lcs-699an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 699. Click here for more information. ,@lcs-700an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 700. Click here for more information. ,@lcs-701an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 701. Click here for more information.   CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=2.4
eRMSD7The ERMSD action with label eRMSD7 calculates the following quantities:
 Quantity   
 Type   
 Description  
eRMSD7
scalar
the eRMSD between the instantaneous structure and the reference structure that was input: ERMSDCalculate eRMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../helix-templates/CAG_686-688_c246_o.pdb ATOMSthe list of atoms (use lcs)=@lcs-686an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 686. Click here for more information. ,@lcs-687an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 687. Click here for more information. ,@lcs-688an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 688. Click here for more information. ,@lcs-695an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 695. Click here for more information. ,@lcs-696an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 696. Click here for more information. ,@lcs-697an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 697. Click here for more information. 
eRMSD7: ERMSDCalculate eRMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../helix-templates/CAG_686-688_c246_o.pdb ATOMSthe list of atoms (use lcs)=@lcs-686an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 686. Click here for more information. ,@lcs-687an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 687. Click here for more information. ,@lcs-688an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 688. Click here for more information. ,@lcs-695an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 695. Click here for more information. ,@lcs-696an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 696. Click here for more information. ,@lcs-697an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 697. Click here for more information.   CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=2.4
eRMSD8The ERMSD action with label eRMSD8 calculates the following quantities:
 Quantity   
 Type   
 Description  
eRMSD8
scalar
the eRMSD between the instantaneous structure and the reference structure that was input: ERMSDCalculate eRMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../helix-templates/CCUCU_762-766_c246_o.pdb ATOMSthe list of atoms (use lcs)=@lcs-762an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 762. Click here for more information. ,@lcs-763an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 763. Click here for more information. ,@lcs-764an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 764. Click here for more information. ,@lcs-765an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 765. Click here for more information. ,@lcs-766an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 766. Click here for more information. ,@lcs-771an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 771. Click here for more information. ,@lcs-772an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 772. Click here for more information. ,@lcs-773an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 773. Click here for more information. ,@lcs-774an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 774. Click here for more information. ,@lcs-775an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 775. Click here for more information. 
eRMSD8: ERMSDCalculate eRMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../helix-templates/CCUCU_762-766_c246_o.pdb ATOMSthe list of atoms (use lcs)=@lcs-762an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 762. Click here for more information. ,@lcs-763an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 763. Click here for more information. ,@lcs-764an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 764. Click here for more information. ,@lcs-765an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 765. Click here for more information. ,@lcs-766an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 766. Click here for more information. ,@lcs-771an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 771. Click here for more information. ,@lcs-772an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 772. Click here for more information. ,@lcs-773an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 773. Click here for more information. ,@lcs-774an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 774. Click here for more information. ,@lcs-775an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 775. Click here for more information.   CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=2.4
eRMSD9The ERMSD action with label eRMSD9 calculates the following quantities:
 Quantity   
 Type   
 Description  
eRMSD9
scalar
the eRMSD between the instantaneous structure and the reference structure that was input: ERMSDCalculate eRMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../helix-templates/GGA_836-838_c246_o.pdb ATOMSthe list of atoms (use lcs)=@lcs-836an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 836. Click here for more information. ,@lcs-837an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 837. Click here for more information. ,@lcs-838an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 838. Click here for more information. ,@lcs-852an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 852. Click here for more information. ,@lcs-853an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 853. Click here for more information. ,@lcs-854an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 854. Click here for more information. 
eRMSD9: ERMSDCalculate eRMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../helix-templates/GGA_836-838_c246_o.pdb ATOMSthe list of atoms (use lcs)=@lcs-836an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 836. Click here for more information. ,@lcs-837an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 837. Click here for more information. ,@lcs-838an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 838. Click here for more information. ,@lcs-852an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 852. Click here for more information. ,@lcs-853an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 853. Click here for more information. ,@lcs-854an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 854. Click here for more information.   CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=2.4
eRMSD10The ERMSD action with label eRMSD10 calculates the following quantities:
 Quantity   
 Type   
 Description  
eRMSD10
scalar
the eRMSD between the instantaneous structure and the reference structure that was input: ERMSDCalculate eRMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../helix-templates/GCCUUG_422-427_c246_o.pdb ATOMSthe list of atoms (use lcs)=@lcs-422an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 422. Click here for more information. ,@lcs-423an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 423. Click here for more information. ,@lcs-424an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 424. Click here for more information. ,@lcs-425an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 425. Click here for more information. ,@lcs-426an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 426. Click here for more information. ,@lcs-427an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 427. Click here for more information. ,@lcs-434an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 434. Click here for more information. ,@lcs-435an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 435. Click here for more information. ,@lcs-436an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 436. Click here for more information. ,@lcs-437an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 437. Click here for more information. ,@lcs-438an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 438. Click here for more information. ,@lcs-439an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 439. Click here for more information. 
eRMSD10: ERMSDCalculate eRMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../helix-templates/GCCUUG_422-427_c246_o.pdb ATOMSthe list of atoms (use lcs)=@lcs-422an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 422. Click here for more information. ,@lcs-423an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 423. Click here for more information. ,@lcs-424an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 424. Click here for more information. ,@lcs-425an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 425. Click here for more information. ,@lcs-426an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 426. Click here for more information. ,@lcs-427an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 427. Click here for more information. ,@lcs-434an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 434. Click here for more information. ,@lcs-435an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 435. Click here for more information. ,@lcs-436an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 436. Click here for more information. ,@lcs-437an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 437. Click here for more information. ,@lcs-438an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 438. Click here for more information. ,@lcs-439an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 439. Click here for more information.   CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=2.4
eRMSD11The ERMSD action with label eRMSD11 calculates the following quantities:
 Quantity   
 Type   
 Description  
eRMSD11
scalar
the eRMSD between the instantaneous structure and the reference structure that was input: ERMSDCalculate eRMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../helix-templates/UGG_616-618_c246_o.pdb ATOMSthe list of atoms (use lcs)=@lcs-616an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 616. Click here for more information. ,@lcs-617an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 617. Click here for more information. ,@lcs-618an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 618. Click here for more information. ,@lcs-661an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 661. Click here for more information. ,@lcs-662an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 662. Click here for more information. ,@lcs-663an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 663. Click here for more information. 
eRMSD11: ERMSDCalculate eRMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../helix-templates/UGG_616-618_c246_o.pdb ATOMSthe list of atoms (use lcs)=@lcs-616an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 616. Click here for more information. ,@lcs-617an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 617. Click here for more information. ,@lcs-618an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 618. Click here for more information. ,@lcs-661an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 661. Click here for more information. ,@lcs-662an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 662. Click here for more information. ,@lcs-663an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 663. Click here for more information.   CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=2.4
eRMSD12The ERMSD action with label eRMSD12 calculates the following quantities:
 Quantity   
 Type   
 Description  
eRMSD12
scalar
the eRMSD between the instantaneous structure and the reference structure that was input: ERMSDCalculate eRMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../helix-templates/GGC_840-842_c246_o.pdb ATOMSthe list of atoms (use lcs)=@lcs-840an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 840. Click here for more information. ,@lcs-841an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 841. Click here for more information. ,@lcs-842an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 842. Click here for more information. ,@lcs-849an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 849. Click here for more information. ,@lcs-850an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 850. Click here for more information. ,@lcs-851an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 851. Click here for more information. 
eRMSD12: ERMSDCalculate eRMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../helix-templates/GGC_840-842_c246_o.pdb ATOMSthe list of atoms (use lcs)=@lcs-840an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 840. Click here for more information. ,@lcs-841an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 841. Click here for more information. ,@lcs-842an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 842. Click here for more information. ,@lcs-849an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 849. Click here for more information. ,@lcs-850an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 850. Click here for more information. ,@lcs-851an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 851. Click here for more information.   CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=2.4


RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=eRMSD1 ATthe position of the restraint=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=500.0
RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=eRMSD2 ATthe position of the restraint=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=500.0
RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=eRMSD3 ATthe position of the restraint=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=500.0
RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=eRMSD4 ATthe position of the restraint=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=500.0
RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=eRMSD5 ATthe position of the restraint=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=500.0
RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=eRMSD6 ATthe position of the restraint=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=500.0
RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=eRMSD7 ATthe position of the restraint=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=500.0
RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=eRMSD8 ATthe position of the restraint=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=500.0
RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=eRMSD9 ATthe position of the restraint=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=500.0
RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=eRMSD10 ATthe position of the restraint=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=500.0
RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=eRMSD11 ATthe position of the restraint=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=500.0
RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=eRMSD12 ATthe position of the restraint=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=500.0

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=eRMSD1 STRIDE the frequency with which the quantities of interest should be output=100 FILEthe name of the file on which to output these quantities=COLVAR_36-39
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=eRMSD2 STRIDE the frequency with which the quantities of interest should be output=100 FILEthe name of the file on which to output these quantities=COLVAR_530-532
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=eRMSD3 STRIDE the frequency with which the quantities of interest should be output=100 FILEthe name of the file on which to output these quantities=COLVAR_664-666
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=eRMSD4 STRIDE the frequency with which the quantities of interest should be output=100 FILEthe name of the file on which to output these quantities=COLVAR_669-672
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=eRMSD5 STRIDE the frequency with which the quantities of interest should be output=100 FILEthe name of the file on which to output these quantities=COLVAR_679-681
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=eRMSD6 STRIDE the frequency with which the quantities of interest should be output=100 FILEthe name of the file on which to output these quantities=COLVAR_682-684
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=eRMSD7 STRIDE the frequency with which the quantities of interest should be output=100 FILEthe name of the file on which to output these quantities=COLVAR_686-688
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=eRMSD8 STRIDE the frequency with which the quantities of interest should be output=100 FILEthe name of the file on which to output these quantities=COLVAR_762-766
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=eRMSD9 STRIDE the frequency with which the quantities of interest should be output=100 FILEthe name of the file on which to output these quantities=COLVAR_836-838
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=eRMSD10 STRIDE the frequency with which the quantities of interest should be output=100 FILEthe name of the file on which to output these quantities=COLVAR_422-427
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=eRMSD11 STRIDE the frequency with which the quantities of interest should be output=100 FILEthe name of the file on which to output these quantities=COLVAR_616-618
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=eRMSD12 STRIDE the frequency with which the quantities of interest should be output=100 FILEthe name of the file on which to output these quantities=COLVAR_840-842