From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Nov 02 2015 - 07:47:25 CST
Hi Haleh,
This could be a problem with Windows end-of-line characters. If your files
are created in a text editor under Windows, try processing them with
dos2unix on the cluster before running the calculation.
Jerome
On 2 November 2015 at 12:55, Haleh a <halehabdi_at_sabanciuniv.edu> wrote:
> Dear NAMD users,
>
> Recently, I have been trying to run ABF simulations with RMSD as the
> collective variables. I am using the following *.in file:
>
> #rmsd.in
> Colvarstrajfrequency 1000
> Colvarsrestartfrequency 1000
> colvar {
> name RMSD
> width 0.05
> lowerboundary 0.1
> upperboundary 1.25
> lowerwallconstant 100.0
> upperwallconstant 100.0
> outputAppliedForce on
>
> rmsd {
> atoms {
> psfSegID P1
> atomNameResidueRange CA 1-159
> atomsFile main_abf.pdb
> atomsCol B
> atomsColValue 1.0
> }
> refPositionsFile ref_abf.pdb
> refPositionsCol B
> refPositionsColValue 1.0
> }
> }
>
> abf {
> colvars RMSD
> fullSamples 1000
> }
>
> I am getting the following error on NAMD 2.10 on a cluster :
>
> colvars:
> ----------------------------------------------------------------------
> colvars: Initializing the collective variables module, version 2012-03-23.
> colvars: # analysis = off [default]
> colvars: # colvarsTrajFrequency = 1000
> colvars: # colvarsRestartFrequency = 1000
> colvars: # colvarsTrajAppend = off [default]
> colvars: The restart output state file will be "abf.colvars.state".
> colvars: The final output state file will be "abfo.colvars.state".
> colvars: The trajectory file will be "abfo.colvars.traj".
> colvars:
> ----------------------------------------------------------------------
> colvars: Initializing a new collective variable.
> colvars: # name = RMSD
> colvars: Initializing a new "rmsd" component.
> colvars: # componentCoeff = 1 [default]
> colvars: # componentExp = 1 [default]
> colvars: # period = 0 [default]
> colvars: # wrapAround = 0 [default]
> colvars: Error: definition for atom group "atoms" not found.
> colvars: If this error message is unclear, try recompiling with
> -DCOLVARS_DEBUG.
> FATAL ERROR: Error in the collective variables module: exiting.
>
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: Error in the collective variables module: exiting.
>
>
> I tried running the same script on NAMD 2.9 on my desktop. It does not
> give me the same error. However, my Abf.colvar.state and abf.pmf files are
> empty as follows:
>
> abf.pmf file:
>
> xi A(xi)
> 0.1 0
> 0.15 0
> 0.2 0
> 0.25 0
> 0.3 0
> 0.35 0
> 0.4 0
> 0.45 0
> 0.5 0
> 0.55 0
> 0.6 0
> 0.65 0
> 0.7 0
> 0.75 0
> 0.8 0
> 0.85 0
> 0.9 0
> 0.95 0
> 1 0
> 1.05 0
> 1.1 0
> 1.15 0
> 1.2 0
> 1.25 0
>
>
> and
>
> Abf.colvar.state
>
> configuration {
> step 1104000
> dt 1.00000000000000e+000
> }
>
> colvar {
> name RMSD
> x 1.56341258634097e+000
> }
>
> abf {
> configuration {
> name abf1
> }
> samples
> 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0
>
> gradient
> 0 0 0
> 0 0 0
> 0 0 0
> 0 0 0
> 0 0 0
> 0 0 0
> 0 0 0
> 0 0
> }
>
> Any suggestion to remove the error and help me get more clear on the
> subject is highly appreciated.
>
>
> Best regards,
> Haleh
>
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