From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Aug 03 2012 - 15:16:46 CDT
Hello Rui, I need also the NAMD configuration file, because "run 10000" is
not exactly the same as "numsteps 10000".
Thanks
Giacomo
On Fri, Aug 3, 2012 at 11:30 AM, Rui Zhang <zhangrui1002_at_gmail.com> wrote:
> Hi Giacomo,
> It was run for 10,000 steps. And the colvars configuration file is:
>
> colvarsTrajFrequency 100
> colvarsRestartFrequency 10000
>
> colvar {
> name BaseDist
>
> distance {
> group1 {
> atomnumbers { 21 27 28 }
> }
> group2 {
> atomnumbers { 59746 59747 59749 }
> }
> }
> corrfunc on
> corrfunctype coordinate
> corrfunclength 1000
> }
>
> colvar {
> name LysCoorNum
>
> distance {
> group1 {
> atomnumbers { 27 }
> }
> group2 {
> atomnumbers { 9831 }
> }
> }
> corrfunc on
> corrfunctype coordinate
> corrfunclength 1000
> }
>
> analysis on
>
> Thank you!
> Rui
>
> On Thu, Aug 2, 2012 at 6:15 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>wrote:
>
>> Hello Rui, can you send the number of simulation steps, or even better
>> the other configuration files? You can send them off list if you prefer.
>>
>> Giacomo
>>
>>
>> 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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