Re: no output for corrfunc

From: Robert Elder (robert.elder_at_colorado.edu)
Date: Thu Nov 01 2012 - 18:26:23 CDT

Hi Giacomo,

I'm having the same issue with the colvars autocorrelation file not being
written (as in the conversation below). Could you forward me the patch or
suggest another workaround?

Thanks,
Robert Elder

On Mon, Aug 6, 2012 at 10:20 AM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>wrote:

> 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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