[gmx-users] energy minimization breaks freeze group apart

Patricia Francis-Lyon patflyon at hotmail.com
Wed Jan 30 01:13:52 CET 2008

My issue :
>> 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. 
Xavier Periole wrote:>You might want to solvate your system before minimization ... the>modeled loop might appreciate some solvent around!
Thanks Xavier, you were right! When I solvated before doing energy minimization
on the loop, the freeze group did not break apart.
I wrote:
>> 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.
Xavier Periole wrote:
>.Could that simply be the result of periodic boundary conditions?
I don't understand why the problem arose, why solvating before loop minimization 
ameliorated it, and what it has to do with periodic boundary conditions. Could someone explain?
Also, I still have an issue with how Gromacs is building my system. when I run 
editconf -f  $protName.gro  -o box.gro -d 1.2 -bt dodecahedron
Gromacs places the solute in the top corner of the box, rather than
centering it in the box. Shouldn't it be in the center? What am I doing wrong?
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