On 05/07/11, balaji nagarajan <[email protected]> wrote: > > > > <!-- > .hmmessage P > { > margin:0px; > padding:0px > } > body.hmmessage > { > font-size: 10pt; > font-family:Tahoma > } > --> > > > > > > > > Dear Users ! > > I have a doubt in minimizing the structure with water box ! > > > >
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? :-) > > > > 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 ! > > > > Maybe it was near a minimum already. Maybe the solvent is locking the protein in place. Maybe it doesn't matter. > > > > 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 ) > > > > That depends on the purpose. Do check out all the tutorial material you can put your hands on. Google is your friend. > > > > when i have the option 6 of the file ( Coulomb-14 ) for the first step and > the last step ! > > > > What's your question? Mark > > > > > 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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