# Re: Multi canonical ensemble method

From: Takeru KAMEDA (kamedapon_at_hiroshima-u.ac.jp)
Date: Wed Oct 30 2019 - 00:26:28 CDT

Hi Jerome.

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#24897

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

________________________________________

CC: namd-l

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>> 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%7C637054410151677447&sdata=rWfUPJdN2KjCG78tilAQa%2B4fGUzllIGohj%2FsQTT8PBo%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<
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

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2020 - 23:17:12 CST