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:
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:
Thank you for your advice.
I changed the method orientation to spinAngle.
Now I'm trying such method.
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,
________________________________________
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,
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:
Hi. I am trying multi-canonical ensemble method using NAMD2.13.
I wrote colvar file as follows:
colvarsTrajFrequency 5000
colvar {
outputValue on
orientation {
abf {
Then, we execute simulation, following error was output:
colvars: ----------------------------------------------------------------------
Any parts of configulation file was wrong?
Best wishes,
This archive was generated by hypermail 2.1.6
: Tue Dec 31 2019 - 23:21:00 CST
https://raw.githubusercontent.com/Colvars/colvars/master/tests/spinangle.in
26868d8e12640d3750%7C1%7C0%7C637085568234920878&sdata=soTnsL1ev1023QcQwGrqktuaU1TLk92cFx00B3PPUwA%3D&reserved=0>>
Hi Jerome.
And, sorry for the late reply.
https://www.ks.uiuc.edu/Research/namd/2.13/ug/node55.html#24897
234930867&sdata=D88d4MWTzKi%2Fw2Atyjk5rNhWkB5%2BqEQxH7kx2M3a2pc%3D&reserved=0>>
However, I can not set "axis" part in "List of keywords" of spinAngle.
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
Jerome
Dear all.
colvarsRestartFrequency 50000
name theta
#outputVelocity on
#outputEnergy on
#outputSystemForce on
#outputAppliedForce on
atoms { atomnumbers {
13754 13755 13756 13757 13758 13761 13783 13785 19290 19291 19292 19293 19294 19297 19319 19321
}}
refPositionsFile ./colvar.pdb
refPositionsCol O
}
}
colvars theta
fullSamples 200
hideJacobian
}
colvars: Initializing the collective variables module, version 2018-10-16.
colvars: Please cite Fiorin et al, Mol Phys 2013:
colvars: http://dx.doi.org/10.1080/00268976.2013.813594
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
oshima-u.ac.jp%7Cf27084172a614d43e33e08d7459c5a6e%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637054410151677447&sdata=LJa3HRG3d3Dm8g91Di2YvRf5owBoU%2F8jCjT3Mzk1680%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%7C637085568234970844&sdata=3d1h%2FiNeL9Hzk3KElhniiMNQYqvKGRxT%2FJtOsUW7XW4%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%7C637080422187048867&sdata=j6GeGCLQRPbtIOYvjRC5J9rErGcUyK9QCcuOqG7WPH4%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%7C637085568234980839&sdata=H7hoGAWkNu2sJdWx63GIshDVUqfK%2B8vkYtWyaW!
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.
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