From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Wed Jun 20 2012 - 15:59:20 CDT
Hi Shaon,
Thank you for the report, this was indeed a bug. A fix is on its way,
and will be included in the next update to the colvars code.
Best,
Jerome
On 20 June 2012 13:32, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr> wrote:
> 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
>> }
>> }
>> ****************************************************
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