Ensure that job parameter settings in jgmtAMMU.sh . Check parameters in igwhAMMV.dat . Jobfile is jgmtAMA.sh. Number of solvent molecules read. Set NTB to -1 for a truncated octahedron, solute is rotated and translated.
Output is AMAfullbox.dat and oboxAMA.out .
Before starting a MD simulation strain should be removed from the system with a short energy minimization. The Atomic Reference Positions for restraining are identical to the initial system coordinates. Solute atom positions should be positionally restrained to let only the solvent relax. For switch values during warmup see table VII-45. Output is omd1ama.out and amamd1finc.dat .