Project ID: plumID:19.001
Source: plumed-g3.dat
Originally used with PLUMED version: 2.4
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
tested onv2.10
tested onmaster
# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 
# choose units - by default PLUMED uses kj/mol, nm, and ps
# UNITS ENERGY=kcal/mol LENGTH=A
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=ref.pdb
RANDOM_EXCHANGESSet random pattern for exchanges. More details
FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=1000

INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=cv-s.dat

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# RESTRAINS, CONSTRAINS definition
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eRMSD_start: ...
  ERMSDCalculate eRMSD with respect to a reference structure. This action has hidden defaults. More details
  ATOMSthe list of atoms (use lcs)=@lcs-1an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 1. Click here for more information. ,@lcs-2an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information. ,@lcs-3an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information. ,@lcs-4an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information. ,@lcs-5an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information. ,@lcs-7an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information. ,@lcs-8an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information. ,@lcs-9an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. Click here for more information. ,@lcs-10an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 10. Click here for more information. ,@lcs-11an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 11. Click here for more information. ,@lcs-12an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 12. Click here for more information. ,@lcs-13an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 13. Click here for more information. ,@lcs-14an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 14. Click here for more information. ,@lcs-15an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 15. Click here for more information. ,@lcs-16an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 16. Click here for more information. ,@lcs-17an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 17. Click here for more information. ,@lcs-18an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 18. Click here for more information. ,@lcs-19an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 19. Click here for more information. ,@lcs-20an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 20. Click here for more information. ,@lcs-21an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 21. Click here for more information. ,@lcs-22an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 22. Click here for more information. ,@lcs-23an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 23. Click here for more information. ,@lcs-24an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 24. Click here for more information. ,@lcs-25an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 25. Click here for more information. ,@lcs-26an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 26. Click here for more information. ,@lcs-27an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 27. Click here for more information. ,@lcs-28an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 28. Click here for more information. ,@lcs-29an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 29. Click here for more information. ,@lcs-30an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 30. Click here for more information. ,@lcs-31an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 31. Click here for more information. ,@lcs-32an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 32. Click here for more information. ,@lcs-33an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 33. Click here for more information. ,@lcs-34an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 34. Click here for more information. ,@lcs-35an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 35. Click here for more information. ,@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-40an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 40. Click here for more information. ,@lcs-41an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 41. Click here for more information. 
  REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=ref.pdb
...

u-wall_LPR: ...
  UPPER_WALLSDefines a wall for the value of one or more collective variables, More details
  ARGthe arguments on which the bias is acting=d1_lp1,d2_lp1,d3_lp1 ATthe positions of the wall=0.30,0.30,0.30 KAPPAthe force constant for the wall=500.0,500.0,500.0 EXP the powers for the walls=2,2,2 EPS the values for s_i in the expression for a wall=1,1,1 OFFSET the offset for the start of the wall=0,0,0
...

l-wall_aLPR: ...
  LOWER_WALLSDefines a wall for the value of one or more collective variables, More details
  ARGthe arguments on which the bias is acting=a1_lp1,a2_lp1,a3_lp1,a4_lp1,a5_lp1 ATthe positions of the wall=2.75,2.75,2.75,2.75,2.75 KAPPAthe force constant for the wall=100.0,100.0,100.0,100.0,100.0 EXP the powers for the walls=2,2,2,2,2 EPS the values for s_i in the expression for a wall=1,1,1,1,1 OFFSET the offset for the start of the wall=0,0,0,0,0
...

LBP-rest: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=1328,1329,1330,1334,1336,1338,1339,1340,1341,1342 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=1,3,6,8,9,11,12,14,16,17,20,21,22,23,25,27,29,1296,1297,1300,1302,1303,1305,1306,1308,1309,1310,1311,1312,1314,1315,1318,1319,1320,1322,1324,1326 LOWEST this flag allows you to recover the lowest of these variables

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# WALLS (PES/FES restrictions)
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u-wall_eRMSD_start: ...
  UPPER_WALLSDefines a wall for the value of one or more collective variables, More details
  ARGthe arguments on which the bias is acting=eRMSD_start ATthe positions of the wall=0.6 KAPPAthe force constant for the wall=5000.0
...
 
l-wall_LBP-rest: ...
  LOWER_WALLSDefines a wall for the value of one or more collective variables, More details
  ARGthe arguments on which the bias is acting=LBP-rest.lowest ATthe positions of the wall=0.8 KAPPAthe force constant for the wall=5000.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0
...

u-wall_d-3: ...
  UPPER_WALLSDefines a wall for the value of one or more collective variables, More details
  ARGthe arguments on which the bias is acting=d-3 ATthe positions of the wall=1.0 KAPPAthe force constant for the wall=50.0
...
 
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# METADYNAMICS
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metad: ...
  METADUsed to performed metadynamics on one or more collective variables. More details
  ARGthe labels of the scalars on which the bias will act=d-3 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=298.16 BIASFACTORuse well tempered metadynamics and use this bias factor=5 PACEthe frequency for hill addition=500 HEIGHTthe heights of the Gaussian hills=1.0 SIGMAthe widths of the Gaussian hills=0.02
  GRID_MINthe lower bounds for the grid=0.01 GRID_MAXthe upper bounds for the grid=50.0 GRID_SPARSE use a sparse grid to store hills FILE a file in which the list of added hills is stored=HILLS_SRP-motif_BzCN
...

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# OUTPUTS
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PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d-3,eRMSD_start,LBP-rest.lowest,metad.bias STRIDE the frequency with which the quantities of interest should be output=10 FILEthe name of the file on which to output these quantities=COLVAR_SRP-motif_BzCN
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=u-wall_d-3.bias,l-wall_LBP-rest.bias,u-wall_eRMSD_start.bias STRIDE the frequency with which the quantities of interest should be output=10 FILEthe name of the file on which to output these quantities=RESTR_BIAS_SRP-motif_BzCN