[gmx-users] minimization_error

[balaji nagarajan]

Dear Users ! 

I have a doubt in minimizing the structure with water box ! 

I have taken a penta peptide and solvated it with spce water box ! 

I have minimized the system with the minim.mdp file which i have attached ! ( i have used steep option ) 

when I calculated the protein- protein and protein-solvent interaction energy 

the protein-protein energy have not fall down much ! 

and i tried with various options in the mdp options " emtol "


(how to know that the system is entirely minimized ! what is the criteria to be fixed on regarding a 
small peptide )


when i have the option 6 of the file ( Coulomb-14 ) for the first step and the last step ! 

Statistics over 1 steps [ 0.0000 through 0.0000 ps ], 1 data sets
All statistics are over 1 points

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Coulomb-14                  908.433         --          0          0  (kJ/mol)






Statistics over 1000 steps [ 0.0000 through 999.0000 ps ], 1 data sets
All statistics are over 2 points

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Coulomb-14                    892.2        2.3        nan   -16.4675  (kJ/mol)


------------------------------------------------------------------------
I have attached all the files below ! 

the script  "test-script.sh " is to run all which i have done ! 

thanks in advance 


 		 	   		  
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