Re: colvars: Error: in parsing "centers"

From: Giacomo Fiorin (giacomo.fiorin_at_temple.edu)
Date: Thu Jun 10 2010 - 21:10:55 CDT

Hi Leonardo, you have to specify one center for each variable, for a total
of four in your case.

Giacomo

---- ----
 Dr. Giacomo Fiorin
 ICMS - Institute for Computational Molecular Science - Temple University
 1900 N 12 th Street, Philadelphia, PA 19122
 giacomo.fiorin_at_temple.edu
---- ----

On Thu, Jun 10, 2010 at 8:25 PM, Leonardo Herrera <ldhz04_at_yahoo.com.mx>wrote:

> Hi user's
> I have a plomen when I am runing simulation with colvars. I don't
> understand this error. Can somebody help me?
> the error is this
> ...
> ...
> colvars: Initializing a new "harmonic" instance.
> colvars: # name = "harmonic1" [default]
> colvars: # colvars = { cu1500, cu1501, cu1502, cu1503 }
> colvars: Applying this bias to collective variable "cu1500".
> colvars: Applying this bias to collective variable "cu1501".
> colvars: Applying this bias to collective variable "cu1502".
> colvars: Applying this bias to collective variable "cu1503".
> colvars: # forceConstant = 50
> colvars: The force constant for colvar "cu1500" will be rescaled to 5000
> according to the specified width.
> colvars: The force constant for colvar "cu1501" will be rescaled to 5000
> according to the specified width.
> colvars: The force constant for colvar "cu1502" will be rescaled to 5000
> according to the specified width.
> colvars: The force constant for colvar "cu1503" will be rescaled to 5000
> according to the specified width.
> colvars: Error: in parsing "centers".
> FATAL ERROR: Error in the collective variables module: exiting.
> ..
> ..
> ..
> and my colvar script is TrajFrequency 100
> colvarsRestartFrequency 100
>
> colvar {
> name cu1500
> width 0.1
> lowerboundary 0.0
> upperboundary 0.5
> lowerWallConstant 100.0
> upperWallConstant 100.0
> distance {
> group1 {
> atomnumbers { 9232 }
> }
> group2 {
> atomnumbers { 983 1626 6794 }
> }
> }
> }
>
> colvar {
> name cu1501
> width 0.1
> lowerboundary 0.0
> upperboundary 0.5
> lowerWallConstant 100.0
> upperWallConstant 100.0
> distance {
> group1 {
> atomnumbers { 9233 }
> }
> group2 {
> atomnumbers { 1654 5998 6766 }
> }
> }
> }
> ..
> ...
> .....
> harmonic {
> colvars cu1500 cu1501 cu1502 cu1503
> centers 2.5
> forceConstant 50.0
> }
>
> tahnks in avance.
>
> MenB Leonardo David Herrera Zúñiga POSGRADO EN QUÍMICA UAMI
> Biofisicoquímica Universidad Autonoma Metropolitana IztapalapaTel. +52 (55)
> 5804 4674 ldhz04_at_yahoo.com.mx

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