# Open SourceMolecular Dynamics

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exercises:2016_ethz_mmm:geometry_optimization

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 exercises:2016_ethz_mmm:geometry_optimization [2016/02/03 09:54]127.0.0.1 external edit exercises:2016_ethz_mmm:geometry_optimization [2016/02/25 12:06] (current)sclelia 2016/02/25 12:06 sclelia 2016/02/03 09:54 external edit 2016/02/25 12:06 sclelia 2016/02/03 09:54 external edit Line 1: Line 1: ====== Geometry Optimization ====== ====== Geometry Optimization ====== - In this exercise you will run a geometry optimization calculation,​ for two Xe atoms placed at distance $r=3.00Å$. + In this exercise you will run a geometry optimization calculation,​ for two Kr atoms placed at distance $r=3.00Å$. === 1. Step === === 1. Step === Line 20: Line 20: &​NONBONDED &​NONBONDED &​LENNARD-JONES &​LENNARD-JONES - atoms Xe Xe + atoms Kr Kr - EPSILON ​   [K_e] 232 + EPSILON ​   [K_e] 164.56 - SIGMA [angstrom] ​  3.98 + SIGMA [angstrom] ​  3.601 RCUT  [angstrom] ​ 25.0 RCUT  [angstrom] ​ 25.0 &END LENNARD-JONES &END LENNARD-JONES &END NONBONDED &END NONBONDED &CHARGE &CHARGE - ATOM Xe + ATOM Kr CHARGE 0.0 CHARGE 0.0 &END CHARGE &END CHARGE Line 45: Line 45: &​COORD &​COORD UNIT angstrom UNIT angstrom - ​Xe  0 0 0 + ​Kr  0 0 0 - ​Xe  3 0 0 + ​Kr  3 0 0 &​END COORD &​END COORD &END SUBSYS &END SUBSYS Line 74: Line 74: === 5. Step: Checking the energy === === 5. Step: Checking the energy === - In the geopt.out file you have a list of energies, one for each geometry optimization step that was performed. The overall energy should decrease, ​untill ​the minimum. + In the geopt.out file you have a list of energies, one for each geometry optimization step that was performed. The overall energy should decrease, ​until the minimum. To check it, you can simply search the geopt.out file with the ''​grep''​ command: To check it, you can simply search the geopt.out file with the ''​grep''​ command: <​code>​ <​code>​