[gmx-users] Re:realloc Error !

Mark Abraham Mark.Abraham at anu.edu.au
Sun Mar 4 23:15:39 CET 2007

Qiang Zhong wrote:
>   I have a complex protein which is predicted from cluspro server,I use it as a
> start structure,I want to know the complex will deformated to a new conformation
> which is NMR experiment result(it only include a fragment of protein).So I want to
> know the two protein interaction information by MD.
>   I use energy minimize step to get optimize structure,but there Fmax always >1.So
> I don't know how to do!

You need an adequately minimized structure, but you won't be able to get 
  Fmax of zero. "Adequate" just means that later when you heat the 
system and do your equilibration run that things do not fall apart.

>   Otherwise,I got another error message in same situation:
> Fatal error:
> Box was shifted at least 10 times. Please see log-file.

When? During the minimization? What was different between when you got 
this error message and when you didn't?

>   I also don't know how to understand it.
>   Could you tell me reason?Thank you very much! 

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