[gmx-users] minimization_error

[Mark Abraham]

On 05/07/11, balaji nagarajan  <balaji_sethu at hotmail.com> wrote:
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> Dear Users ! 
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> I have a doubt in minimizing the structure with water box ! 
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Go easy on the exclamation marks - who's going to attract a higher quality answer, someone who sounds like a mature professional, or an excited kid? :-)


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> I have taken a penta peptide and solvated it with spce water box ! 
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> I have minimized the system with the minim.mdp file which i have attached ! ( i have used steep option ) 
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> when I calculated the protein- protein and protein-solvent interaction energy 
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> the protein-protein energy have not fall down much ! 
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Maybe it was near a minimum already. Maybe the solvent is locking the protein in place. Maybe it doesn't matter.


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> and i tried with various options in the mdp options " emtol "
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> (how to know that the system is entirely minimized ! what is the criteria to be fixed on regarding a 
> small peptide )
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That depends on the purpose. Do check out all the tutorial material you can put your hands on. Google is your friend.


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> when i have the option 6 of the file ( Coulomb-14 ) for the first step and the last step ! 
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What's your question?

Mark

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> Statistics over 1 steps [ 0.0000 through 0.0000 ps ], 1 data sets
> All statistics are over 1 points
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> Energy                      Average   Err.Est.       RMSD  Tot-Drift
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> Coulomb-14                  908.433         --          0          0  (kJ/mol)
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> Statistics over 1000 steps [ 0.0000 through 999.0000 ps ], 1 data sets
> All statistics are over 2 points
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> Energy                      Average   Err.Est.       RMSD  Tot-Drift
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> Coulomb-14                    892.2        2.3        nan   -16.4675  (kJ/mol)
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> I have attached all the files below ! 
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> the script  "test-script.sh " is to run all which i have done ! 
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> thanks in advance 
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