Re: Metadynamics with eigenvector

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Aug 25 2014 - 10:17:22 CDT

Hello Nicolas, please put the vector components in the (x,y,z) format or
provide a PDB or XYZ file that contains them.

Giacomo

On Mon, Aug 25, 2014 at 10:40 AM, Nicolas Floquet <
nicolas.floquet_at_univ-montp1.fr> wrote:

> Hello all !
>
> i'm trying to use a vector (eigen vector) as the reaction coordinate for a
> metadynamics.
>
> here's my colvar file :
>
> colvarsTrajFrequency 10000
> colvar {
> name r1
> lowerBoundary -5.0
> lowerWallConstant 50.0
> upperBoundary 5.0
> upperWallConstant 50.0
> width 0.05
> outputVelocity off
> outputAppliedForce off
> eigenvector {
> atoms {atomNumbersRange 1-2} # I PUT HERE ONLY TWO ATOMS FOR TESTING
> refPositionsFile ./test.pdb # CONTAINS THE TWO ATOMS subjected to the
> vecotr IN THE PDB FORMAT
> vector -0.00088 0.00061 0.00092 -0.00105 0.00063 0.00098 # THE 3N
> COMPONENTS OF THE EIGEN VECTOR
> }
> }
> metadynamics {
> name metadyn_r
> colvars r1
> usegrids on
> hillWeight 0.01 # Default is 0.01 - higher numbers = faster
> dumpFreeEnergyFile yes
> newHillFrequency 100 # Default is 100 - lower numbers = faster
> }
>
> Please help me, the error message is :
>
> colvars: Initializing a new collective variable.
> colvars: # name = r1
> colvars: Initializing a new "eigenvector" component.
> colvars: # componentCoeff = 1 [default]
> colvars: # componentExp = 1 [default]
> colvars: # period = 0 [default]
> colvars: # wrapAround = 0 [default]
> colvars: Initializing atom group "atoms".
> colvars: Atom group "atoms" defined, 2 initialized: total mass =
> 13.019.
> colvars: # refPositions = [default]
> colvars: # refPositionsFile = ./test.pdb
> colvars: # refPositionsCol = "" [default]
> colvars: # vector =
> colvars: Using vector components from input file.
> colvars: Error: vector components do not match the number of requested
> atoms.
> colvars: If this error message is unclear, try recompiling with
> -DCOLVARS_DEBUG.
> FATAL ERROR: Error in the collective variables module: exiting.
>
> Thank you in advance for your help.
>
> Nicolas
>
>

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