From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Aug 06 2012 - 11:20:37 CDT
Hello Rui, I found the error: sorry about the inconvenience. In the last
code change of the section that writes final output files some time ago,
the coorFunc-related output was accidentally disabled.
Can you recompile NAMD? If so, I could send you a patch that fixes this
temporarily.
On Thu, Aug 2, 2012 at 8:06 PM, Rui Zhang <zhangrui1002_at_gmail.com> wrote:
> Hi,
> I was trying to calculation the auto-correlation function for a colvar.
> But the corrfunc.dat file was produced even though the calculation was
> finished successfully. And the output showed:
>
> colvars: Initializing a new collective variable.
> colvars: # name = Lysdist
> colvars: Initializing a new "distance" component.
> colvars: # componentCoeff = 1 [default]
> colvars: # componentExp = 1 [default]
> colvars: # period = 0 [default]
> colvars: # wrapAround = 0 [default]
> colvars: # forceNoPBC = off [default]
> colvars: # oneSiteSystemForce = off [default]
> colvars: Initializing atom group "group1".
> colvars: Atom group "group1" defined, 1 initialized: total mass =
> 15.9994.
> colvars: Initializing atom group "group2".
> colvars: Atom group "group2" defined, 1 initialized: total mass =
> 14.007.
> colvars: All components initialized.
> colvars: # width = 1 [default]
> colvars: # lowerBoundary = 0 [default]
> colvars: # lowerWallConstant = 0 [default]
> colvars: # upperBoundary = 0 [default]
> colvars: # upperWallConstant = 0 [default]
> colvars: # expandBoundaries = off [default]
> colvars: # extendedLagrangian = off [default]
> colvars: # outputValue = on [default]
> colvars: # outputVelocity = off [default]
> colvars: # outputSystemForce = off [default]
> colvars: # outputAppliedForce = off [default]
> colvars: # runAve = off [default]
> colvars: # corrFunc = on
> colvars: # corrFuncWithColvar = "Lysdist" [default]
> colvars: Calculating auto-correlation function.
> colvars: # corrFuncType = coordinate
> colvars: # corrFuncOffset = 0 [default]
> colvars: # corrFuncLength = 1000
> colvars: # corrFuncStride = 1 [default]
> colvars: # corrFuncNormalize = on [default]
> colvars: # corrFuncOutputFile = "stats2.Lysdist.corrfunc.dat" [default]
>
> Could you help me check why there's no output for corrfunc? Thank you!
>
> Rui
>
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