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Regression test for lambda-ABF in NAMD
Had to force single-thread calculation to work around unreliable results on the singel timestep level
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namd/tests/interface/009_lambda_dynamics/AutoDiff/test.colvars.out
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,122 @@ | ||
| colvars: ---------------------------------------------------------------------- | ||
| colvars: Please cite Fiorin et al, Mol Phys 2013: | ||
| colvars: https://doi.org/10.1080/00268976.2013.813594 | ||
| colvars: as well as all other papers listed below for individual features used. | ||
| colvars: This version was built with the C++11 standard or higher. | ||
| colvars: Summary of compile-time features available in this build: | ||
| colvars: - SMP parallelism: enabled (num. threads = 1) | ||
| colvars: - Lepton custom functions: available | ||
| colvars: - Tcl interpreter: available | ||
| colvars: Redefining the Tcl "cv" command to the new script interface. | ||
| colvars: The restart output state file will be "test.tmp.colvars.state". | ||
| colvars: The final output state file will be "test.colvars.state". | ||
| colvars: ---------------------------------------------------------------------- | ||
| colvars: Reading new configuration from file "test.in": | ||
| colvars: # units = "" [default] | ||
| colvars: # smp = on [default] | ||
| colvars: # colvarsTrajFrequency = 1 | ||
| colvars: # colvarsRestartFrequency = 10 | ||
| colvars: # scriptedColvarForces = off [default] | ||
| colvars: # scriptingAfterBiases = off [default] | ||
| colvars: # sourceTclFile = "" [default] | ||
| colvars: ---------------------------------------------------------------------- | ||
| colvars: Initializing a new collective variable. | ||
| colvars: # name = "lambda" | ||
| colvars: Initializing a new "alchLambda" component. | ||
| colvars: # name = "" [default] | ||
| colvars: # componentCoeff = 1 [default] | ||
| colvars: # componentExp = 1 [default] | ||
| colvars: # period = 0 [default] | ||
| colvars: # wrapAround = 0 [default] | ||
| colvars: # forceNoPBC = off [default] | ||
| colvars: # scalable = on [default] | ||
| colvars: All components initialized. | ||
| colvars: # timeStepFactor = 1 [default] | ||
| colvars: # width = 1 [default] | ||
| colvars: # lowerBoundary = 0 | ||
| colvars: # upperBoundary = 1 | ||
| colvars: # hardLowerBoundary = off [default] | ||
| colvars: # hardUpperBoundary = off [default] | ||
| colvars: # expandBoundaries = off [default] | ||
| colvars: # extendedLagrangian = on | ||
| colvars: Enabling the extended Lagrangian term for colvar "lambda". | ||
| colvars: # extendedTemp = 300 [default] | ||
| colvars: # extendedMass = 150000 | ||
| colvars: # outputEnergy = off [default] | ||
| colvars: # extendedLangevinDamping = 1 [default] | ||
| colvars: # reflectingLowerBoundary = on | ||
| colvars: # reflectingUpperBoundary = on | ||
| colvars: # outputValue = on [default] | ||
| colvars: # outputVelocity = off [default] | ||
| colvars: # outputTotalForce = on | ||
| colvars: # outputAppliedForce = on | ||
| colvars: # subtractAppliedForce = off [default] | ||
| colvars: # runAve = off [default] | ||
| colvars: # corrFunc = off [default] | ||
| colvars: ---------------------------------------------------------------------- | ||
| colvars: Collective variables initialized, 1 in total. | ||
| colvars: ---------------------------------------------------------------------- | ||
| colvars: Initializing a new "abf" instance. | ||
| colvars: # name = "abf1" [default] | ||
| colvars: # colvars = { lambda } | ||
| colvars: # stepZeroData = off [default] | ||
| colvars: # outputEnergy = off [default] | ||
| colvars: # outputFreq = 10 [default] | ||
| colvars: # timeStepFactor = 1 [default] | ||
| colvars: # applyBias = on [default] | ||
| colvars: # hideJacobian = off [default] | ||
| colvars: Jacobian (geometric) forces will be included in reported free energy gradients. | ||
| colvars: # fullSamples = 0 | ||
| colvars: # minSamples = 0 [default] | ||
| colvars: # inputPrefix = [default] | ||
| colvars: # historyFreq = 0 [default] | ||
| colvars: # shared = off [default] | ||
| colvars: # updateBias = on [default] | ||
| colvars: # maxForce = [default] | ||
| colvars: # integrate = on [default] | ||
| colvars: Finished ABF setup. | ||
| colvars: ---------------------------------------------------------------------- | ||
| colvars: Collective variables biases initialized, 1 in total. | ||
| colvars: ---------------------------------------------------------------------- | ||
| colvars: Collective variables module (re)initialized. | ||
| colvars: ---------------------------------------------------------------------- | ||
| colvars: Updating NAMD interface: | ||
| colvars: updating atomic data (0 atoms). | ||
| colvars: updating group data (0 scalable groups, 0 atoms in total). | ||
| colvars: updating grid object data (0 grid objects in total). | ||
| colvars: | ||
| colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: | ||
| colvars: | ||
| colvars: - BAOA integrator: | ||
| colvars: BouRabee2010 https://doi.org/10.1137/090758842 | ||
| colvars: | ||
| colvars: - Colvars module: | ||
| colvars: - Colvars-NAMD interface: | ||
| colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 | ||
| colvars: | ||
| colvars: - ABF colvar bias implementation: | ||
| colvars: - Internal-forces free energy estimator: | ||
| colvars: Henin2010 https://doi.org/10.1021/ct9004432 | ||
| colvars: | ||
| colvars: - alchLambda colvar component: | ||
| colvars: Lagardere2023 https://arxiv.org/abs/2307.08006 | ||
| colvars: | ||
| colvars: - NAMD engine: | ||
| colvars: Phillips2020 https://doi.org/10.1063/5.0014475 | ||
| colvars: | ||
| colvars: updating target temperature (T = 300 K). | ||
| colvars: Updating NAMD interface: | ||
| colvars: updating atomic data (0 atoms). | ||
| colvars: updating group data (0 scalable groups, 0 atoms in total). | ||
| colvars: updating grid object data (0 grid objects in total). | ||
| colvars: updating target temperature (T = 300 K). | ||
| colvars: Current simulation parameters: initial step = 0, integration timestep = 1 | ||
| colvars: Updating atomic parameters (masses, charges, etc). | ||
| colvars: The restart output state file will be "test.tmp.colvars.state". | ||
| colvars: Initializing extended coordinate to colvar value. | ||
| colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". | ||
| colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". | ||
| colvars: Saving collective variables state to "test.tmp.colvars.state". | ||
| colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". | ||
| colvars: Saving collective variables state to "test.tmp.colvars.state". | ||
| colvars: Saving collective variables state to "test.colvars.state". |
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namd/tests/interface/009_lambda_dynamics/AutoDiff/test.colvars.state.stripped
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| configuration { | ||
| step 20 | ||
| dt 1.000000e+00 | ||
| } | ||
|
|
||
| colvar { | ||
| name lambda | ||
| x 0.20245122980265 | ||
| extended_x 0.20245122980265 | ||
| extended_v 0.00015391572142221 | ||
| } | ||
|
|
||
| abf { | ||
| configuration { | ||
| step 20 | ||
| name abf1 | ||
| } | ||
|
|
||
| samples | ||
| 20 | ||
|
|
||
| gradient | ||
| -8.0141711538951 | ||
| } | ||
|
|
22 changes: 22 additions & 0 deletions
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namd/tests/interface/009_lambda_dynamics/AutoDiff/test.colvars.traj
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,22 @@ | ||
| # step lambda ft_lambda fa_lambda | ||
| 0 2.00000000000000e-01 0.00000000000000e+00 0.00000000000000e+00 | ||
| 1 1.99992395820152e-01 7.96684221784716e+00 -7.96684221784716e+00 | ||
| 2 1.99901022015639e-01 7.88324824580072e+00 -7.92504523182394e+00 | ||
| 3 1.99800875537990e-01 7.80665457013810e+00 -7.88558167792866e+00 | ||
| 4 1.99762218563404e-01 7.73048537492151e+00 -7.84680760217688e+00 | ||
| 5 1.99769367689661e-01 7.65449840553533e+00 -7.80834576284857e+00 | ||
| 6 1.99807952653923e-01 7.58324655116611e+00 -7.77082922756816e+00 | ||
| 7 1.99845484395962e-01 7.52736002846028e+00 -7.73604791340989e+00 | ||
| 8 1.99869775547569e-01 7.50005661145498e+00 -7.70654900066553e+00 | ||
| 9 1.99836075126736e-01 7.51578941134210e+00 -7.68535349074070e+00 | ||
| 10 1.99812694785606e-01 7.57995782043818e+00 -7.67481392371045e+00 | ||
| 11 1.99873218443446e-01 7.69049228724148e+00 -7.67623922948600e+00 | ||
| 12 2.00011013975393e-01 7.84032662263539e+00 -7.68991317891511e+00 | ||
| 13 2.00168434974116e-01 8.01767282114353e+00 -7.71512545908653e+00 | ||
| 14 2.00359096146772e-01 8.20385566003222e+00 -7.75003475915408e+00 | ||
| 15 2.00679173048730e-01 8.37628507963051e+00 -7.79178478051917e+00 | ||
| 16 2.01074279279389e-01 8.52227734901836e+00 -7.83744056605037e+00 | ||
| 17 2.01467672933468e-01 8.63554749590671e+00 -7.88438803251251e+00 | ||
| 18 2.01869356438853e-01 8.71184768812576e+00 -7.93035801337991e+00 | ||
| 19 2.02221179933948e-01 8.75639425563999e+00 -7.97383360507781e+00 | ||
| 20 2.02451229802647e-01 8.78058458142414e+00 -8.01417115389513e+00 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,4 @@ | ||
| # 1 | ||
| # 0.00000000000000e+00 1.00000000000000e+00 1 0 | ||
|
|
||
| 5.00000000000000e-01 20 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,4 @@ | ||
| # 1 | ||
| # 0.00000000000000e+00 1.00000000000000e+00 1 0 | ||
|
|
||
| 5.00000000000000e-01 -8.01417115389513e+00 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,5 @@ | ||
| # 1 | ||
| # -5.00000000000000e-01 1.00000000000000e+00 2 0 | ||
|
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| 0.00000000000000e+00 8.01417115389513e+00 | ||
| 1.00000000000000e+00 0.00000000000000e+00 |
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namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.colvars.out
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,126 @@ | ||
| colvars: ---------------------------------------------------------------------- | ||
| colvars: Please cite Fiorin et al, Mol Phys 2013: | ||
| colvars: https://doi.org/10.1080/00268976.2013.813594 | ||
| colvars: as well as all other papers listed below for individual features used. | ||
| colvars: This version was built with the C++11 standard or higher. | ||
| colvars: Summary of compile-time features available in this build: | ||
| colvars: - SMP parallelism: enabled (num. threads = 1) | ||
| colvars: - Lepton custom functions: available | ||
| colvars: - Tcl interpreter: available | ||
| colvars: Redefining the Tcl "cv" command to the new script interface. | ||
| colvars: The restart output state file will be "test.restart.tmp.colvars.state". | ||
| colvars: The final output state file will be "test.restart.colvars.state". | ||
| colvars: ---------------------------------------------------------------------- | ||
| colvars: Reading new configuration from file "test.in": | ||
| colvars: # units = "" [default] | ||
| colvars: # smp = on [default] | ||
| colvars: # colvarsTrajFrequency = 1 | ||
| colvars: # colvarsRestartFrequency = 10 | ||
| colvars: # scriptedColvarForces = off [default] | ||
| colvars: # scriptingAfterBiases = off [default] | ||
| colvars: # sourceTclFile = "" [default] | ||
| colvars: ---------------------------------------------------------------------- | ||
| colvars: Initializing a new collective variable. | ||
| colvars: # name = "lambda" | ||
| colvars: Initializing a new "alchLambda" component. | ||
| colvars: # name = "" [default] | ||
| colvars: # componentCoeff = 1 [default] | ||
| colvars: # componentExp = 1 [default] | ||
| colvars: # period = 0 [default] | ||
| colvars: # wrapAround = 0 [default] | ||
| colvars: # forceNoPBC = off [default] | ||
| colvars: # scalable = on [default] | ||
| colvars: All components initialized. | ||
| colvars: # timeStepFactor = 1 [default] | ||
| colvars: # width = 1 [default] | ||
| colvars: # lowerBoundary = 0 | ||
| colvars: # upperBoundary = 1 | ||
| colvars: # hardLowerBoundary = off [default] | ||
| colvars: # hardUpperBoundary = off [default] | ||
| colvars: # expandBoundaries = off [default] | ||
| colvars: # extendedLagrangian = on | ||
| colvars: Enabling the extended Lagrangian term for colvar "lambda". | ||
| colvars: # extendedTemp = 300 [default] | ||
| colvars: # extendedMass = 150000 | ||
| colvars: # outputEnergy = off [default] | ||
| colvars: # extendedLangevinDamping = 1 [default] | ||
| colvars: # reflectingLowerBoundary = on | ||
| colvars: # reflectingUpperBoundary = on | ||
| colvars: # outputValue = on [default] | ||
| colvars: # outputVelocity = off [default] | ||
| colvars: # outputTotalForce = on | ||
| colvars: # outputAppliedForce = on | ||
| colvars: # subtractAppliedForce = off [default] | ||
| colvars: # runAve = off [default] | ||
| colvars: # corrFunc = off [default] | ||
| colvars: ---------------------------------------------------------------------- | ||
| colvars: Collective variables initialized, 1 in total. | ||
| colvars: ---------------------------------------------------------------------- | ||
| colvars: Initializing a new "abf" instance. | ||
| colvars: # name = "abf1" [default] | ||
| colvars: # colvars = { lambda } | ||
| colvars: # stepZeroData = off [default] | ||
| colvars: # outputEnergy = off [default] | ||
| colvars: # outputFreq = 10 [default] | ||
| colvars: # timeStepFactor = 1 [default] | ||
| colvars: # applyBias = on [default] | ||
| colvars: # hideJacobian = off [default] | ||
| colvars: Jacobian (geometric) forces will be included in reported free energy gradients. | ||
| colvars: # fullSamples = 0 | ||
| colvars: # minSamples = 0 [default] | ||
| colvars: # inputPrefix = [default] | ||
| colvars: # historyFreq = 0 [default] | ||
| colvars: # shared = off [default] | ||
| colvars: # updateBias = on [default] | ||
| colvars: # maxForce = [default] | ||
| colvars: # integrate = on [default] | ||
| colvars: Finished ABF setup. | ||
| colvars: ---------------------------------------------------------------------- | ||
| colvars: Collective variables biases initialized, 1 in total. | ||
| colvars: ---------------------------------------------------------------------- | ||
| colvars: Collective variables module (re)initialized. | ||
| colvars: ---------------------------------------------------------------------- | ||
| colvars: Updating NAMD interface: | ||
| colvars: updating atomic data (0 atoms). | ||
| colvars: updating group data (0 scalable groups, 0 atoms in total). | ||
| colvars: updating grid object data (0 grid objects in total). | ||
| colvars: | ||
| colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: | ||
| colvars: | ||
| colvars: - BAOA integrator: | ||
| colvars: BouRabee2010 https://doi.org/10.1137/090758842 | ||
| colvars: | ||
| colvars: - Colvars module: | ||
| colvars: - Colvars-NAMD interface: | ||
| colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 | ||
| colvars: | ||
| colvars: - ABF colvar bias implementation: | ||
| colvars: - Internal-forces free energy estimator: | ||
| colvars: Henin2010 https://doi.org/10.1021/ct9004432 | ||
| colvars: | ||
| colvars: - alchLambda colvar component: | ||
| colvars: Lagardere2023 https://arxiv.org/abs/2307.08006 | ||
| colvars: | ||
| colvars: - NAMD engine: | ||
| colvars: Phillips2020 https://doi.org/10.1063/5.0014475 | ||
| colvars: | ||
| colvars: updating target temperature (T = 300 K). | ||
| colvars: ---------------------------------------------------------------------- | ||
| colvars: Loading state from text file "test.colvars.state". | ||
| colvars: Restarting collective variable "lambda" from value: 0.202451 | ||
| colvars: Restarted abf bias "abf1" with step number 20. | ||
| colvars: ---------------------------------------------------------------------- | ||
| colvars: Updating NAMD interface: | ||
| colvars: updating atomic data (0 atoms). | ||
| colvars: updating group data (0 scalable groups, 0 atoms in total). | ||
| colvars: updating grid object data (0 grid objects in total). | ||
| colvars: updating target temperature (T = 300 K). | ||
| colvars: Current simulation parameters: initial step = 20, integration timestep = 1 | ||
| colvars: Updating atomic parameters (masses, charges, etc). | ||
| colvars: The restart output state file will be "test.restart.tmp.colvars.state". | ||
| colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". | ||
| colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". | ||
| colvars: Saving collective variables state to "test.restart.tmp.colvars.state". | ||
| colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". | ||
| colvars: Saving collective variables state to "test.restart.tmp.colvars.state". | ||
| colvars: Saving collective variables state to "test.restart.colvars.state". |
25 changes: 25 additions & 0 deletions
25
namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.colvars.state.stripped
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| configuration { | ||
| step 40 | ||
| dt 1.000000e+00 | ||
| } | ||
|
|
||
| colvar { | ||
| name lambda | ||
| x 0.20836051020006 | ||
| extended_x 0.20836051020006 | ||
| extended_v 0.0004528018356754 | ||
| } | ||
|
|
||
| abf { | ||
| configuration { | ||
| step 40 | ||
| name abf1 | ||
| } | ||
|
|
||
| samples | ||
| 40 | ||
|
|
||
| gradient | ||
| -9.1800383003581 | ||
| } | ||
|
|
22 changes: 22 additions & 0 deletions
22
namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.colvars.traj
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,22 @@ | ||
| # step lambda ft_lambda fa_lambda | ||
| 20 2.02451229802650e-01 0.00000000000000e+00 -8.01417115389510e+00 | ||
| 21 2.02544063317688e-01 8.79677173742116e+00 -8.05143784834872e+00 | ||
| 22 2.02557993229958e-01 8.81441210482505e+00 -8.08611849637037e+00 | ||
| 23 2.02568176589621e-01 8.83952439255414e+00 -8.11887527446532e+00 | ||
| 24 2.02645067021906e-01 8.87347035441114e+00 -8.15031673612973e+00 | ||
| 25 2.02773241774165e-01 8.91763592471448e+00 -8.18100950367312e+00 | ||
| 26 2.02938664924388e-01 8.97161705686943e+00 -8.21141748648836e+00 | ||
| 27 2.03109223468217e-01 9.03911380941207e+00 -8.24207290585590e+00 | ||
| 28 2.03273109969140e-01 9.13005964298271e+00 -8.27378671789615e+00 | ||
| 29 2.03385946933364e-01 9.26505411891078e+00 -8.30796835241389e+00 | ||
| 30 2.03516464758499e-01 9.46339797126387e+00 -8.34648267304223e+00 | ||
| 31 2.03738807200153e-01 9.74220853201881e+00 -8.39150608784792e+00 | ||
| 32 2.04047164987984e-01 1.01132685590046e+01 -8.44531116507157e+00 | ||
| 33 2.04385089669305e-01 1.05741725498844e+01 -8.50982211612650e+00 | ||
| 34 2.04767813595167e-01 1.10964359033778e+01 -8.58589899222213e+00 | ||
| 35 2.05293465871353e-01 1.16275890959526e+01 -8.67280442375728e+00 | ||
| 36 2.05909736002440e-01 1.21203178221254e+01 -8.76856868482306e+00 | ||
| 37 2.06541843034024e-01 1.25351891085928e+01 -8.87036923681684e+00 | ||
| 38 2.07201416018228e-01 1.28409084557337e+01 -8.97485711099886e+00 | ||
| 39 2.07831424699300e-01 1.30323135766731e+01 -9.07889445627256e+00 | ||
| 40 2.08360510200055e-01 1.31246482196932e+01 -9.18003830035808e+00 |
4 changes: 4 additions & 0 deletions
4
namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.count
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,4 @@ | ||
| # 1 | ||
| # 0.00000000000000e+00 1.00000000000000e+00 1 0 | ||
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| 5.00000000000000e-01 40 |
4 changes: 4 additions & 0 deletions
4
namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.grad
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,4 @@ | ||
| # 1 | ||
| # 0.00000000000000e+00 1.00000000000000e+00 1 0 | ||
|
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| 5.00000000000000e-01 -9.18003830035807e+00 |
5 changes: 5 additions & 0 deletions
5
namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.pmf
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,5 @@ | ||
| # 1 | ||
| # -5.00000000000000e-01 1.00000000000000e+00 2 0 | ||
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| 0.00000000000000e+00 9.18003830035808e+00 | ||
| 1.00000000000000e+00 0.00000000000000e+00 |
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| @@ -0,0 +1,11 @@ | ||
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| langevin on | ||
| langevinTemp 300.0 | ||
| langevinDamping 0.000000001 | ||
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| alch on | ||
| alchType TI | ||
| alchFile ../Common/da.pdb | ||
| alchCol B | ||
| alchLambda 0.2 | ||
|
|
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| @@ -0,0 +1,3 @@ | ||
| Info: NAMD 3.1alpha2 for Linux-x86_64-multicore | ||
| colvars: Initializing the collective variables module, version 2024-06-04. | ||
| colvars: Using NAMD interface, version "2023-12-05". |
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