[gmx-users] Re:realloc Error !

[Qiang Zhong]

Mark:   
  Thank you for your advice,I always get one of these error message,
in same situation. I find that when I got box shift error message,there are
many lincs warning. I did not find some special message for memory not enough
error message.
  
  
> Qiang Zhong :
> >   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! 
> 
> Please be aware that in typed English, spaces are used after punctuation 
> marks like commas, periods and interrogation marks (i.e. ',', '.', '?') 
> in order to make the text easier to read.
> 
> Mark