Dynamics and geometry optimization with ChemShell

More documents

Recommendations

Info

Small Molecules: newopt – zopt Optimisation of a molecule given as z-matrix using the BFGS method: newopt \ function= zopt : { \ zmatrix= water.zz4 \ theory= mndo } \ method= bfgs Johannes Kästner STFC Daresbury Lab Large Molecules: HDLCopt ● Small molecule, redundant internals: hdlcopt coords=c \ residues= [ res_selectall coords=c ] \ theory= mndo ● Large molecule, provided as pdb file, HDLCs: set residues [ pdb_to_res 1PBE.pdb ] hdlcopt coords=c \ residues= $residues \ constraints= {{bond 3 5} {angle 3 5 6}} \ theory= mndo Johannes Kästner STFC Daresbury Lab 8
Dimer Method for TS search ● Dimer: two images of the system, constant distance ● Rotation: difference of the forces ● Movement: − In dimer direction: against the force − Perpendicular to dimer direction: along the force ● Converges to first-order saddle points ● No Hessian required: for large systems Johannes Kästner STFC Daresbury Lab Dimer method in <strong>ChemShell</strong> dimer coords=c mode=3 \ maxcyc=100 \ theory= gamess : $gamess_args Johannes Kästner STFC Daresbury Lab 9
Page 1 and 2: L6 Geometry Optimization and Dynami
Page 3 and 4: Free-energy differences: ● Umbrel
Page 5 and 6: Coordinate Systems ● Cartesian co
Page 7: Optimisers in ChemShell Four optimi
Page 11 and 12: Molecular Dynamics in ChemShell NVE
Page 13 and 14: Umbrella Sampling ● A number of w
Page 15 and 16: Setup of QM/MM calculations of prot

Dynamics and geometry optimization with ChemShell

Create successful ePaper yourself

Delete template?

Save as template?