dPCA input question

[MamtaMohan]

Hi,

I am try to do Metadynamics using dPCA as collective variable.

I am not clear about VectorNumber input.

I used CARMA to generate input and this is my input file:

colvars: ---------------------------------------------------------------------- colvars: Initializing the collective variables module, version 2012-03-23. colvars: # analysis = on colvars: # colvarsTrajFrequency = 1000 colvars: # colvarsRestartFrequency = 1000 colvars: # colvarsTrajAppend = off [default] colvars: The restart output state file will be "T4L72131_mBkdPCA1bar_out.restart.colvars.state". colvars: The final output state file will be "T4L72131_mBkdPCA1bar_out.colvars.state". colvars: The trajectory file will be "T4L72131_mBkdPCA1bar_out.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = dpca72 colvars: Initializing a new "dihedralPC" component. colvars: # componentCoeff = 1 [default] colvars: # componentExp = 1 [default] colvars: # period = 0 [default] colvars: # wrapAround = 0 [default] colvars: # psfSegID = PROA colvars: # vectorFile = carma.mBkdPCA1bar.eigenvectors.dat colvars: # vectorNumber = 1 colvars: Error: wrong number of coefficients: 652. Expected 8 (4 coeffs per residue, minus one residue). colvars: If this error message is unclear, try recompiling with -DCOLVARS_DEBUG. FATAL ERROR: Error in the collective variables module: exiting.

I would appreciate your response.

Mamta

[jhenin]

Either the file format produced by CARMA changed, or the atom definitions you provided to CARMA don't match those provided to colvars. Here colvars has detected only three residues, but it parses the CARMA file as containing much more data. How many residues did you analyze in CARMA?

[MamtaMohan]

Dear Jerome,

Thank you for your response.

I used all 164 residues of protein to generate dPCA eigenvector file via CARMA as an input for 'vectorFile'.

For 'vectorFile', it looks like after reading your question that input for 'vectorFile' need to be generated only for three residues which are given in the residueRange. Is this correct?

My understanding is not clear about input for 'vectorNumber'.

In COLVAR documentation it says 'File containing dihedralPCA eigenvector(s). Acceptable Values: positive integer'. So I gave '1' to do pseudo-potential calculation only along 1st dPCA component. Is this input correct or I am suppose to provide a file?

I am not quiet sure which file I need to provide for 'vectorNumber'. I would appreciate your input.

I am listing my colvar file below. If you could point my mistakes I would truly appreciate it.

Mamta

colvar.conf #

MetaD Standard

T4L72131 backbone dPCA

# colvarsTrajFrequency 1000 colvarsRestartFrequency 1000 analysis on

colvar { name dpca72 outputVelocity on outputAppliedForce on runAve on

dihedralPC { residueRange 71 - 73 psfSegID PROA hBondCoeff 0.5 angleRef 88.0 angleTol 15.0 hBondCutoff 3.3 hBondExpNumer 6 hBondExpDenom 8 vectorFile carma.mBkdPCA1bar.eigenvectors.dat vectorNumber 1

metadynamics { name metaD_BkdPCA1bar colvars dpca72 hillWidth 1.25331 # Default = 1.25331 hillweight 0.01 # Default = 0.01, higher number = faster =poor sampling newHillFrequency 100 # Default = 100, lower numbers = faster = poor sampling dumpFreeEnergyFile yes writeHillsTrajectory on }

} }

[jhenin]

This line looks wrong:

residueRange 71 - 73

You probably want

residueRange 1 - 164

[MamtaMohan]

Thank you for your help.