From: Rui Zhang (zhangrui1002_at_gmail.com)
Date: Fri Aug 03 2012 - 15:53:47 CDT
Hi Giacomo,
The namd configuration file concerning the number of steps is below.
PME on ;# use PME electrostatics
PMEGridSizeX 149 ;# use 147 grid points along
cellbasisVector1
PMEGridSizeY 165 ;# use 165 grid points along
cellbasisVector2
PMEGridSizeZ 150 ;# use 152 grid points along
cellbasisVector3
# ABF SECTION
colvars on
colvarsConfig rxn1.in
outputname $outputname ;# output files with this filename
restartfreq 200 ;# generate a restart file every
500 fs
dcdfreq 1000 ;# write a new dcd file every 500 fs
outputEnergies 1000 ;# output energy every 100 fs
outputPressure 1000 ;# output pressure every 100 fs
outputTiming 1000 ;# output timing every 100 fs
set nSteps 10000
run $nSteps
Thank you!
Rui
On Fri, Aug 3, 2012 at 2:16 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>wrote:
> 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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