Re: Problem of 'missing stage' in colvars.state file

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Wed Jun 20 2012 - 06:32:28 CDT

Hi Shaon,

The "stage" information should be present in the state file if the
bias describes a staged transformation, i.e. if the parameters
targetNumStages or lambdaSchedule are enabled.

If you find inconsistent behavior in this respect, please email me the
colvars config and NAMD log file for that run.

Thank you,
Jerome

On 19 June 2012 19:15, Shaon Chakrabarti <shaonc_at_gmail.com> wrote:
> Hi NAMD experts,
>
>   I am running a simulation with two Colvar components
> and harmonic biases applied to both. When I try to
> restart these simulations using the colvars.state file, I
> face a problem sometimes, that causes the restart to crash.
>
> The error in the log file is the following :
>   "colvars:   Error: current stage is missing from the restart"
>
> I checked the colvars.state file, and indeed, the line with 'stage'
> was missing from one of the colvars component ( please look at
> the colvars.state file contents that I'm pasting below). What
> is surprising however, is that a missing 'stage' does not always
> mean a crashed simulation! Some of the restarts are running
> perfectly even though their colvars.state file had a 'stage' line missing!
>
> Can someone please explain to me what that 'stage' line means
> in the colvars.state file, why it appears in the file sometimes
> but not everytime and why some of the restarts crash when
> the stage line fails to appear?
>
> Thank you,
> Shaon
>
>
> *******colvars.state file for a restart that crashed**********
>
> configuration {
>   step       500000
>   dt 2.000000e+00
> }
>
> colvar {
>   name Rg
>   x  4.19555478295841e+00
> }
>
> colvar {
>   name coord
>   x  8.63693673715731e+02
> }
>
> harmonic {
>   configuration {
>     name umbrella1
>     stage            0
>   }
> }
>
> harmonic {
>   configuration {
>     name umbrella2
>   }
> }
> ****************************************************

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:41 CST