Eew947: Created page with "=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 Research..."

2025-04-21T23:35:03Z

Created page with "=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 *Research..."

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=RNA Statistical Potential with psudoatoms =

*[[Research:RNA SE pseudo atom| Pseudo atom based statistical potential (Zhen and Bell)]]
*[[Research:RNA Statistical Potentials]]
*[[Research:RNA | RNA project 2006 and prior]]
=GB EMP based model =
==GBEMP==
*[[Research:Cg log|CG project log]]
*[[Research:Coarse grain parameter|coarse_grain_parameter_document]]
*[[Research:Amoeba reference frame|Deriving molecular multipoles consistent with inertial frame]]
*[[Research:Coarse grain files|Required Files to run crs simulations]]
*[[Research:Coarse grain mixing|Gay-Berne mixing rules (Methanol)]]
*[[Research:Coarse grain dipeptide|Protein Coarse-grain]]
*[[Research:Coarse grain small|Small Molecule Coarse-grain]]
*[[Research:Dna|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 ==

*[[Research:Coarsegrain dipeptide energy gas|Coarse-grain gas phase Ramachandran map]]
*[[Research:Coarsegrain dipeptide energy solution|Coarse-grain solution phase Ramachandran map]]
*[[Research:All atom dipeptide|all-atom gas phase map]]
*[[Research:All atom dipeptide sol implicit|all-atom solution phase map (from implicit solvent model)]]
*[[Research:All atom dipeptide sol|QM solution phase map]]
*[[Research:All atom dipeptide sole|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

==References==
*[http://dx.doi.org.ezproxy.lib.utexas.edu/10.1021/jp044629q Izvekov, S; Voth, GA. A multiscale coarse-graining method for biomolecular systems. JPC B, 109 (7): 2469-2473 FEB 24 2005]
*[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000827 Voth, 2010]
*[http://dx.doi.org.ezproxy.lib.utexas.edu/10.1016/j.fluid.2010.02.034 Voth, 2010, Fluid Phase Equilibria]

Research:Coarsegrain - Revision history