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
files.tar.gz
Description: GNU Zip compressed data
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