From: 辛志宏 (xzhfood_at_njau.edu.cn)
Date: Wed May 26 2021 - 05:19:28 CDT
Dear namd,
I came across a issue when I run an example according to the namd offical tutorial "Methods for calculating Potentials of Mean Force" by namd3 as follows:
I use NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA
How to fix the issue?
It will be highly appreciate if there are any suggestion.
Zhihong Xin
.........
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version "2020-02-27".
colvars: Please cite Fiorin et al, Mol Phys 2013:
colvars: https://urldefense.com/v3/__https://dx.doi.org/10.1080/00268976.2013.813594__;!!DZ3fjg!tb9uE3bYl5Bfibz8wQRgWaLBW41ITMHSu2NTGRK-qGDGSSmwZONB2m5FTHhpkLQudw$
colvars: in any publication based on this calculation.
colvars: SMP parallelism is enabled; if needed, use "smp off" to override this.
colvars: This version was built with the C++11 standard or higher.
colvars: Using NAMD interface, version "2019-12-04".
colvars: ----------------------------------------------------------------------
colvars: Reading new configuration from file "restrain.in":
colvars: # units = "" [default]
colvars: # smp = on [default]
colvars: # colvarsTrajFrequency = 1000
colvars: # colvarsRestartFrequency = 1000
colvars: # scriptedColvarForces = off [default]
colvars: # scriptingAfterBiases = off [default]
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = "restrain01"
colvars: Initializing a new "distanceXY" 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 "main".
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: Enabling scalable calculation for group "main".
colvars: # printAtomIDs = off [default]
colvars: Atom group "main" defined with 1 atoms requested: total mass = 14.007, total charge = -1.125.
colvars: Initializing atom group "ref".
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: Enabling scalable calculation for group "ref".
colvars: # printAtomIDs = off [default]
colvars: Atom group "ref" defined with 383 atoms requested: total mass = 4600.21, total charge = 21.42.
colvars: # axis = ( 0 , 0 , 1 )
colvars: # oneSiteSystemForce = off [default]
colvars: # oneSiteTotalForce = off [default]
colvars: All components initialized.
colvars: # timeStepFactor = 1 [default]
colvars: # width = 0.5
colvars: # lowerBoundary = 0
colvars: # upperBoundary = 8
colvars: Reading legacy options lowerWall and lowerWallConstant: consider using a harmonicWalls restraint (caution: force constant would then be scaled by width^2).
colvars: # lowerWall = 0 [default]
FATAL ERROR: Error in the collective variables module (see above for details)
colvars: Error: the value of lowerWall must be set explicitly.
FATAL ERROR: Error in the collective variables module (see above for details)
[Partition 0][Node 0] End of program
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