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Analysis and Processing: Convert MD Files<br />
• Convert from AMBER format to GROMOS format: <br />
– GROMOS (van Gunsteren, Berendsen) <br />
• Force field (GROMOS96, GROMOS05) <br />
• Name of an MD simula4on package <br />
– GROMACS (GROningen MAchine for Chemical Simula4ons) <br />
• Rewriben based on GROMOS <br />
• Free so‚ware (GNU general public license) <br />
• QM/MM interface of CPMD <br />
– Classical code <br />
• requires GROMOS format: coordinates (*.g96), topology, input file <br />
– QM part: keyword QMMM in the &CPMD sec4on <br />
&QMMM sec4on <br />
Conversion program:<br />
Conv_7.x (homemade)<br />
• QM/MM calcula4on <br />
– First, equilibrate the system classically using a regular classical MD code <br />
(usually keeping non-‐parametrized parts rigid) <br />
– Define the QM system by assigning pseudopoten4als to selected atoms <br />
– Con4nue equilibra4on with CPMD using MOLECULAR DYNAMICS CLASSICAL <br />
– Wave func4on op4miza4on and normal MOLECULAR DYNAMICS CP
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