Created
June 16, 2023 20:26
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BFEE2 example
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| colvarsTrajFrequency 5000 | |
| colvarsRestartFrequency 5000 | |
| indexFile ../complex.ndx | |
| colvar { | |
| name RMSD | |
| rmsd { | |
| atoms { | |
| indexGroup ligand | |
| } | |
| refpositionsfile ./complex_largeBox.xyz | |
| } | |
| } | |
| colvar { | |
| name eulerTheta | |
| eulerTheta { | |
| atoms { | |
| indexGroup ligand | |
| centerReference on | |
| rotateReference on | |
| centerToOrigin on | |
| enableFitGradients on | |
| fittingGroup { | |
| indexGroup protein | |
| } | |
| refpositionsfile ./complex_largeBox.xyz | |
| } | |
| refpositionsfile ./complex_largeBox.xyz | |
| } | |
| } | |
| colvar { | |
| name eulerPhi | |
| eulerPhi { | |
| atoms { | |
| indexGroup ligand | |
| centerReference on | |
| rotateReference on | |
| centerToOrigin on | |
| enableFitGradients on | |
| fittingGroup { | |
| indexGroup protein | |
| } | |
| refpositionsfile ./complex_largeBox.xyz | |
| } | |
| refpositionsfile ./complex_largeBox.xyz | |
| } | |
| } | |
| colvar { | |
| name eulerPsi | |
| eulerPsi { | |
| atoms { | |
| indexGroup ligand | |
| centerReference on | |
| rotateReference on | |
| centerToOrigin on | |
| enableFitGradients on | |
| fittingGroup { | |
| indexGroup protein | |
| } | |
| refpositionsfile ./complex_largeBox.xyz | |
| } | |
| refpositionsfile ./complex_largeBox.xyz | |
| } | |
| } | |
| colvar { | |
| name polarTheta | |
| customFunction acos(-sin(t / 180 * 3.1415926) * sin(p / 180 * 3.1415926)) * 180 / 3.1415926 | |
| polarTheta { | |
| name t | |
| atoms { | |
| indexGroup ligand | |
| centerReference on | |
| rotateReference on | |
| centerToOrigin on | |
| fittingGroup { | |
| indexGroup protein | |
| } | |
| refpositionsfile ./complex_largeBox.xyz | |
| } | |
| } | |
| polarPhi { | |
| name p | |
| atoms { | |
| indexGroup ligand | |
| centerReference on | |
| rotateReference on | |
| centerToOrigin on | |
| fittingGroup { | |
| indexGroup protein | |
| } | |
| refpositionsfile ./complex_largeBox.xyz | |
| } | |
| } | |
| } | |
| colvar { | |
| name polarPhi | |
| customFunction atan2(cos(t / 180 * 3.1415926), cos(p / 180 * 3.1415926) * sin(t / 180 * 3.1415926)) * 180 / 3.1415926 | |
| period 360 | |
| wrapAround 0.0 | |
| polarTheta { | |
| name t | |
| atoms { | |
| indexGroup ligand | |
| centerReference on | |
| rotateReference on | |
| centerToOrigin on | |
| fittingGroup { | |
| indexGroup protein | |
| } | |
| refpositionsfile ./complex_largeBox.xyz | |
| } | |
| } | |
| polarPhi { | |
| name p | |
| atoms { | |
| indexGroup ligand | |
| centerReference on | |
| rotateReference on | |
| centerToOrigin on | |
| fittingGroup { | |
| indexGroup protein | |
| } | |
| refpositionsfile ./complex_largeBox.xyz | |
| } | |
| } | |
| } | |
| colvar { | |
| name r | |
| width 0.10 | |
| lowerboundary 10.30 | |
| upperboundary 34.30 | |
| reflectingLowerboundary on | |
| reflectingUpperboundary on | |
| subtractAppliedForce on | |
| expandboundaries on | |
| extendedLagrangian on | |
| extendedFluctuation 0.10 | |
| distance { | |
| forceNoPBC yes | |
| group1 { | |
| indexGroup reference | |
| } | |
| group2 { | |
| indexGroup ligand | |
| } | |
| } | |
| } | |
| abf { | |
| colvars r | |
| FullSamples 10000 | |
| historyfreq 50000 | |
| writeCZARwindowFile | |
| } | |
| metadynamics { | |
| colvars r | |
| hillWidth 3.0 | |
| hillWeight 0.05 | |
| wellTempered on | |
| biasTemperature 4000 | |
| } | |
| harmonic { | |
| colvars RMSD | |
| forceConstant 10.0 | |
| centers 0.0 | |
| } | |
| harmonic { | |
| colvars eulerTheta | |
| forceConstant 0.1 | |
| Centers -2.5 | |
| } | |
| harmonic { | |
| colvars eulerPhi | |
| forceConstant 0.1 | |
| Centers -23.5 | |
| } | |
| harmonic { | |
| colvars eulerPsi | |
| forceConstant 0.1 | |
| Centers -12.5 | |
| } | |
| harmonic { | |
| colvars polarTheta | |
| forceConstant 0.1 | |
| Centers 127.5 | |
| } | |
| harmonic { | |
| colvars polarPhi | |
| forceConstant 0.1 | |
| Centers -67.5 | |
| } | |
| colvar { | |
| name translation | |
| distance { | |
| group1 { | |
| indexGroup protein | |
| } | |
| group2 { | |
| dummyAtom (-0.49199315905570984, 0.07393120974302292, 0.7757245898246765) | |
| } | |
| } | |
| } | |
| harmonic { | |
| colvars translation | |
| centers 0.0 | |
| forceConstant 100.0 | |
| } | |
| colvar { | |
| name orientation | |
| orientation { | |
| atoms { | |
| indexGroup protein | |
| } | |
| refPositionsFile ./complex_largeBox.xyz | |
| } | |
| } | |
| harmonic { | |
| colvars orientation | |
| centers (1.0, 0.0, 0.0, 0.0) | |
| forceConstant 2000.0 | |
| } |
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