Re: Multi canonical ensemble method

From: Takeru KAMEDA (kamedapon_at_hiroshima-u.ac.jp)
Date: Wed Nov 06 2019 - 03:58:33 CST

Dear Giacomo.

Thank you for your kind reply.

And, I will take care to keep the list in CC.

I changed parentheses to curly braces as :

axis {1, 0, 0} → axis (1, 0, 0)

Then, following error message were output :

Excerpt below

""""""""
colvars: ----------------------------------------------------------------------
colvars: Collective variables initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "abf" instance.
colvars: # name = "abf1" [default]
colvars: # colvars = { theta }
colvars: # outputEnergy = off [default]
colvars: # timeStepFactor = 1 [default]
colvars: # applyBias = on [default]
colvars: # updateBias = on [default]
colvars: # hideJacobian = on
colvars: Jacobian (geometric) forces will be handled internally.
colvars: # fullSamples = 200
colvars: # inputPrefix = [default]
colvars: # outputFreq = 50000 [default]
colvars: # historyFreq = 0 [default]
colvars: # shared = off [default]
colvars: "total force" in colvar theta requires one of the following features, none of which can be enabled:
colvars: -----------------------------------------
colvars: 1. extended Lagrangian
colvars: User-controlled feature "extended Lagrangian" may not be enabled as a dependency in colvar theta.
colvars: 2. total force calculation
colvars: Dynamic feature unavailable: "Jacobian derivative" in cvc tilt0001.
colvars: ...required by "Jacobian derivative" in colvar theta
colvars: ...required by "total force calculation" in colvar theta
colvars: -----------------------------------------
colvars: ...required by "obtain total force" in bias abf1
colvars: Error: Failed dependency in bias abf1.
FATAL ERROR: Error in the collective variables module: Socket operation on non-socket
""""""""

Are there 2 problems ?

In previous exchange for others, I obtained following manual page

http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#x1-530005.3.3

But, I cloudn't resolve above problem

Thanks.

Best wishes,
Takeru Kameda
PhD Student, Hiroshima University, Japan

________________________________________
差出人: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
送信日時: 2019年11月5日 22:18
宛先: Takeru KAMEDA
CC: NAMD list
件名: Re: namd-l: Multi canonical ensemble method

Hello Takeru, please keep the list in CC.

Your error is due to using curly braces instead of parentheses.

Giacomo

On Mon, Nov 4, 2019 at 9:39 PM Takeru KAMEDA <kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp>> wrote:
Dear Giacomo

Thank you for your kind reply.

I tried ABF as you said using attached files.

However, I obtained attached log file (run.log).

Are there any missing configurauin ?

Thanks

Best wishes,
Takeru Kameda
PhD Student, Hiroshima University, Japan

________________________________________
差出人: Giacomo Fiorin <giacomo.fiorin_at_gmail.com<mailto:giacomo.fiorin_at_gmail.com>>
送信日時: 2019年10月30日 23:22
宛先: Takeru KAMEDA
CC: Jérôme Hénin; namd-l
件名: Re: namd-l: Multi canonical ensemble method

Hello Takeru, it looks like you already found the documentation, try to double-check that your configuration is consistent. See here an example:
https://raw.githubusercontent.com/Colvars/colvars/master/tests/spinangle.inp%7C99bff67013fc40e50bd008d761f2e924%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637085568234920878&sdata=soTnsL1ev1023QcQwGrqktuaU1TLk92cFx00B3PPUwA%3D&reserved=0><https://jpn01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fraw.githubusercontent.com%2FColvars%2Fcolvars%2Fmaster%2Ftests%2Fspinangle.in&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7Cdc8ab578dcfd4144be5308d75d44c110%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637080422187028882&sdata=uDrPerxN1ceCjrQhZ4yfQ9Qpp3xln2AQwhnE4Cs%2B5ak%3D&reserved=0<https://jpn01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fraw.githubusercontent.com%2FColvars%2Fcolvars%2Fmaster%2Ftests%2Fspinangle.in&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C99bff67013fc40e50bd008d761f2e924%7Cc40454ddb26349
26868d8e12640d3750%7C1%7C0%7C637085568234920878&sdata=soTnsL1ev1023QcQwGrqktuaU1TLk92cFx00B3PPUwA%3D&reserved=0>>

If it is consistent with the doc, do you mind pasting it in the email or attaching it?

Giacomo

On Wed, Oct 30, 2019 at 1:28 AM Takeru KAMEDA <kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp><mailto:kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp>>> wrote:
Hi Jerome.

Thank you for your advice.
And, sorry for the late reply.

I changed the method orientation to spinAngle.
https://www.ks.uiuc.edu/Research/namd/2.13/ug/node55.html#24897d008d761f2e924%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637085568234930867&sdata=D88d4MWTzKi%2Fw2Atyjk5rNhWkB5%2BqEQxH7kx2M3a2pc%3D&reserved=0><https://jpn01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ks.uiuc.edu%2FResearch%2Fnamd%2F2.13%2Fug%2Fnode55.html%2324897&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7Cdc8ab578dcfd4144be5308d75d44c110%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637080422187028882&sdata=XY27Nbbf20n3dSyNa%2BJOc7key7RYeJHD3602iGzuaMU%3D&reserved=0<https://jpn01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ks.uiuc.edu%2FResearch%2Fnamd%2F2.13%2Fug%2Fnode55.html%2324897&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C99bff67013fc40e50bd008d761f2e924%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637085568
234930867&sdata=D88d4MWTzKi%2Fw2Atyjk5rNhWkB5%2BqEQxH7kx2M3a2pc%3D&reserved=0>>

Now I'm trying such method.
However, I can not set "axis" part in "List of keywords" of spinAngle.

In this case, I think I must set the axis of rotation and center of roration.

Do you know how to set such axis and center.

Best wishes,
Takeru Kameda
PhD Student, Hiroshima University, Japan

________________________________________
差出人: Jérôme Hénin <jerome.henin_at_ibpc.fr<mailto:jerome.henin_at_ibpc.fr><mailto:jerome.henin_at_ibpc.fr<mailto:jerome.henin_at_ibpc.fr>>>
送信日時: 2019年9月30日 20:49
宛先: Takeru KAMEDA
CC: namd-l
件名: Re: namd-l: Multi canonical ensemble method

Dear Takeru,

this "failed dependency" message indicates that ABF only supports scalar variables. A multidimensional ABF calculation can be done with several scalar variables, not a single vector one.

In this case, the orientation variable is 4-dimensional, which is probably too much for ABF anyway. I recommend reducing your sampling space to 1, 2 or 3 scalar quantities.

Best wishes,
Jerome

On Mon, 30 Sep 2019 at 04:23, Takeru KAMEDA <kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp><mailto:kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp>><mailto:kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp><mailto:kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp>>>> wrote:
Dear all.

Hi. I am trying multi-canonical ensemble method using NAMD2.13.

I wrote colvar file as follows:

colvarsTrajFrequency 5000
colvarsRestartFrequency 50000

colvar {
    name theta

    outputValue on
    #outputVelocity on
    #outputEnergy on
    #outputSystemForce on
    #outputAppliedForce on

    orientation {
        atoms { atomnumbers {
                13754 13755 13756 13757 13758 13761 13783 13785 19290 19291 19292 19293 19294 19297 19319 19321
        }}
        refPositionsFile ./colvar.pdb
        refPositionsCol O
    }
}

abf {
   colvars theta
   fullSamples 200
   hideJacobian
}

Then, we execute simulation, following error was output:

colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2018-10-16.
colvars: Please cite Fiorin et al, Mol Phys 2013:
colvars: http://dx.doi.org/10.1080/00268976.2013.813594640d3750%7C1%7C0%7C637085568234940862&sdata=RMPbHAIKwMTNNhrqaCMzz%2B8C9D4ujwC4SnBH%2Bv%2FVUB8%3D&reserved=0><https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdx.doi.org%2F10.1080%2F00268976.2013.813594&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7Cdc8ab578dcfd4144be5308d75d44c110%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637080422187028882&sdata=XmoQr1L3vQpRC78cVcnJTBoIOdxDMuKsgqMiFa87KuI%3D&reserved=0<https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdx.doi.org%2F10.1080%2F00268976.2013.813594&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C99bff67013fc40e50bd008d761f2e924%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637085568234940862&sdata=RMPbHAIKwMTNNhrqaCMzz%2B8C9D4ujwC4SnBH%2Bv%2FVUB8%3D&reserved=0>><
https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdx.doi.org%2F10.1080%2F00268976.2013.813594&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7Cf27084172a614d43e33e08d7459c5a6e%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637054410151677447&sdata=rWfUPJdN2KjCG78tilAQa%2B4fGUzllIGohj%2FsQTT8PBo%3D&reserved=0<https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdx.doi.org%2F10.1080%2F00268976.2013.813594&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C99bff67013fc40e50bd008d761f2e924%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637085568234950855&sdata=zN%2F%2FfArDJUCDBwN6t5aVPSvabYEQgLwKtrRBtHEEMTE%3D&reserved=0><https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdx.doi.org%2F10.1080%2F00268976.2013.813594&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7Cdc8ab578dcfd4144be5308d75d44c110%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637080422187038878&sdata=2pBfCDjzEeNgVGzI4Vvys75ihIU%2B0UmxyZSWbVho7qk%3D&reserved=0<https://jpn01.safelinks.protection.outlook.com/?url=ht!
 tp%3A%2F
%
2Fdx.doi.org%2F10.1080%2F00268976.2013.813594&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C99bff67013fc40e50bd008d761f2e924%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637085568234950855&sdata=zN%2F%2FfArDJUCDBwN6t5aVPSvabYEQgLwKtrRBtHEEMTE%3D&reserved=0>>>
colvars: in any publication based on this calculation.
colvars: SMP parallelism is available.
colvars: Using NAMD interface, version 2018-08-29.
colvars: ----------------------------------------------------------------------
colvars: Reading new configuration from file "colvar.in<https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcolvar.in&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C99bff67013fc40e50bd008d761f2e924%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637085568234960850&sdata=1R0sCKeduqJvUe%2F1IiZY50O%2Bo7yfK2BobWyC7g374iU%3D&reserved=0><https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcolvar.in&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7Cdc8ab578dcfd4144be5308d75d44c110%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637080422187038878&sdata=leM0XqO1VigPxWB0GKsLZLs4xByxyzWptn12gBG%2FhSo%3D&reserved=0<https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcolvar.in&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C99bff67013fc40e50bd008d761f2e924%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637085568234960850&sdata=1R0sCKeduqJvUe%2F1IiZY50O%2Bo7yfK2BobWyC7g374iU%3D&reserved=0>><https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcolvar.in&data=02%7C01%7Ckamedapon%40hir
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 gV2jQ%3D
&
reserved=0>>>":
colvars: # smp = on [default]
colvars: # analysis = off [default]
colvars: # colvarsTrajFrequency = 5000
colvars: # colvarsRestartFrequency = 50000
colvars: # scriptedColvarForces = off [default]
colvars: # scriptingAfterBiases = off [default]
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = "theta"
colvars: Initializing a new "orientation" 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: Initializing atom group "atoms".
colvars: # name = "" [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # atomsOfGroup = "" [default]
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # enableFitGradients = on [default]
colvars: # printAtomIDs = off [default]
colvars: Atom group "atoms" defined, 16 atoms initialized: total mass = 195.991, total charge = -1.86.
colvars: # refPositions = [default]
colvars: # refPositionsFile = "./colvar.pdb"
colvars: # refPositionsCol = "O"
colvars: # refPositionsColValue = 0 [default]
Info: Found 351 unique exclusion lists needing 1152 bytes
Info: Found 351 unique exclusion lists needing 1152 bytes
Info: Found 351 unique exclusion lists needing 1152 bytes
Info: Found 351 unique exclusion lists needing 1152 bytes
colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry.
colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default]
colvars: All components initialized.
colvars: # timeStepFactor = 1 [default]
colvars: # width = 1 [default]
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on
colvars: # outputVelocity = off [default]
colvars: # outputTotalForce = off [default]
colvars: # outputAppliedForce = off [default]
colvars: # subtractAppliedForce = off [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "abf" instance.
colvars: # name = "abf1" [default]
colvars: # colvars = { theta }
colvars: # outputEnergy = off [default]
colvars: # timeStepFactor = 1 [default]
colvars: Static feature "scalar" may not be enabled as a dependency in colvar theta.
colvars: ...required by "require scalar variables" in bias abf1
colvars: Error: Failed dependency in bias abf1.
FATAL ERROR: Error in the collective variables module: exiting.

Any parts of configulation file was wrong?

Best wishes,
Takeru Kameda
PhD Student, Hiroshima University, Japan

--
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU%2FGNlVLld52T7hO%2FMujyhqFG2pZGLJU6%2FKY%3D&reserved=0><https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgoo.gl%2FQ3TBQU&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7Cdc8ab578dcfd4144be5308d75d44c110%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637080422187048867&sdata=pn9CIh3%2B4BczpKFUYxN%2B%2FOMgfus%2F19zYFFq%2BchGf0II%3D&reserved=0<https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgoo.gl%2FQ3TBQU&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C99bff67013fc40e50bd008d761f2e924%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637085568234990833&sdata=Y%2FHFGnAqPJMZmtQ7o3A0QitT4pWiNlZoOm8OYGOFN9Q%3D&reserved=0>>
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--
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD
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