[gmx-users] energy minimization breaks freeze group apart

Xavier Periole X.Periole at rug.nl
Sun Jan 27 12:09:38 CET 2008

On Sat, 26 Jan 2008 21:40:20 -0800
  Patricia Francis-Lyon <patflyon at hotmail.com> wrote:
> I want to do energy minimization on a loop that had been missing and was 
>filled in by  modloop, while freezing the rest of the protein. 
> Before the minimization I have an SO4 ion and 135 water molecules from the 
>crystallography around the protein. After the minimization the protein has 
>been translated in the y direction away from the water and SO4. 

You might want to solvate your system before minimization ... the
modeled loop might appreciate some solvent around!

> My freeze group is :
> 0 & ! 15 which is System and not loop. 
> I’m confused about why part of the freeze group (the protein) is translated 
>away from the other part (So4 + crystal water). This happens with both steep 
>and l-bfgs.

Could that simply be the result of periodic boundary conditions?
> Thanks for your help!
> Patricia Francis-Lyon
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XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands

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