Re: Colvars error

From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Tue Nov 25 2014 - 00:57:45 CST

Dear Users,

Sorry for the last email I soon find out it was problem with my version of NAMD (2.9). We must have 2.10 in order to enable outputCenters options etc.

However I still encounter problems when I switch off the ouputCenters options as the system report to be unstable. I am wondering whether I gave an abnormally big force constant or what actually determines a suitable force constant for harmonic colvars during a umbrella sampling?

Thanks in advance,

Kevin
ukevi_at_gmx.hk

> On 25 Nov, 2014, at 14:10, Kevin C Chan <cchan2242-c_at_my.cityu.edu.hk> wrote:
>
> Dear Users,
>
> I just ran into an issue with colvars parameters,
>
> colvars: ----------------------------------------------------------------------
> colvars: Collective variables initialized, 1 in total.
> colvars: ----------------------------------------------------------------------
> colvars: Initializing a new "harmonic" instance.
> colvars: # name = "harmonic1" [default]
> colvars: # colvars = { ProjectionZ }
> colvars: # outputEnergy = off [default]
> colvars: # forceConstant = 5
> colvars: The force constant for colvar "ProjectionZ" will be rescaled to 20 according to the specified width.
> colvars: # centers = { 40 }
> colvars: # targetCenters = { 40 } [default]
> colvars: # targetForceConstant = 0 [default]
> colvars: # outputCenters = on
> colvars: # outputAccumulatedWork = on
> colvars: Tried to initialize a grid on a variable with undefined boundaries.
> colvars: If this error message is unclear, try recompiling with -DCOLVARS_DEBUG.
> FATAL ERROR: Error in the collective variables module: exiting.
>
> and the relevant input is:
>
> colvar {
> name ProjectionZ
>
> width 0.5
>
> distanceZ {
>
> main {
> atomsFile main.pdb
> atomsCol B
> atomsColValue 1.0
> }
> ref {
> atomsFile ref.pdb
> atomsCol B
> atomsColValue 1.0
> }
> }
> }
>
> harmonic {
> colvars ProjectionZ
> centers 40
> forceConstant 5.0
> outputCenters yes
> outputAccumulatedWork yes
> }
>
> From the Error message, I have no idea what’s up.
>
> Thanks in advance,
>
> Kevin
> ukevi_at_gmx.hk <mailto:ukevi_at_gmx.hk>

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