Research:Coarsegrain
Jump to navigation
Jump to search
RNA Statistical Potential with psudoatoms
- Pseudo atom based statistical potential (Zhen and Bell)
- Research:RNA Statistical Potentials
- RNA project 2006 and prior
GB EMP based model
GBEMP
- CG project log
- coarse_grain_parameter_document
- Deriving molecular multipoles consistent with inertial frame
- Required Files to run crs simulations
- Gay-Berne mixing rules (Methanol)
- Protein Coarse-grain
- Small Molecule Coarse-grain
- Nucleic Acid Coarse-grain
- Research:Multiscale Molecular Modeling Package Overview
- Research:Coarse Grain Visualization
- move multipoles to offisite using movepole.f in ~pren/tinker/tinker-bat/
dipeptide conformational energy
- Coarse-grain gas phase Ramachandran map
- Coarse-grain solution phase Ramachandran map
- all-atom gas phase map
- all-atom solution phase map (from implicit solvent model)
- QM solution phase map
- all-atom solution phase map (from explicit solvent simulation)
multipole units: tinker analyze (em option) output debye and buckinghams for molecular momonets. same as gaussian /g03 readcrsdict.f of our coarse code convert deby, buckinghams to e-ang to use in tinker
tinker atomic multipoles in key file or from analyze (ep) are in electron-bohr and e-bohr**2, they were converted to e-ang in kmpole.f quadrupole devision by 3 is because the formulae we have for interaction energy (by Smith ) is for non-traceless Q. By dividing traceless Q by 3 we can then use the formulae.
Early parameterization
http://biomol.bme.utexas.edu/wiki/index.php/Software:GB_param