Negative Concentration (topic)

[Guenola]

Date: Thu, 31 Jul 2008 15:59:43 -0400
Subject: Negative Concentration

Hello,

I got negative concentration for one specie and I can manage to understand why?
(rate should be positive...)
Could it be a mistake from Copasi ;) ?
or if not
How can I check/understand this ?
Thanks

Guenola


PS: I noticed that the 'predefined' report: 'steady-state' for Parameter Scan is not working well
(we get only one steady state and not all)
I created another report to get all my values

[shoops]

Date: Thu, 31 Jul 2008 16:14:16 -0400
Subject: Re: Negative Concentration

Hello Guenola,

> Hello,
>
> I got negative concentration for one specie and I can manage to understand why?
> (rate should be positive...)
> Could it be a mistake from Copasi ;) ?

I assume that you are talking about negative concentrations when calculating a steady state. We have had a recent [http://www.copasi.org/tracker/show_bug.cgi?id=1048|issue], which has been fixed in the upcoming release. If your model is correct you can bypass the problem by setting the method parameter "Use Newton" to 0. The Newton Method does not guaranty positive concentrations or volumes. We have added a check which is on by default (Accept Negative Concentration = 0). This check does fail in some situations when using the Newton method.

>
> PS: I noticed that the 'predefined' report: 'steady-state' for Parameter Scan is not working well
> (we get only one steady state and not all)

To get a steady state fro each scanned parameter set please remove the mark on the check box "output from subtask".

Thanks,
Stefan