[Cdk-devel] molecular dynamics and energy minimization module

[Teng L. <ha...@us...>]

Joerg and CDK team,
  Thanks for your email, joerg. You could send email to tl...@nd.... 
  To be honest, molecular dynamics and energy minimization module may become a toy of cdk :-)
  I am now designing the ForceFiledManager which can handle different forcefileds, such as Charmm and AMBER forcefields. In those forcefiled, they use C* or N* to represent the atom type, so your idea of using SMARTS based PATTY assignments is really a good idea. That means we need a forcefiled parser family. Anyway, we coulde delegate the responsibility of building model and setting the right force constant to model builder. Therefore, molecular dynamics  and energy minimization  module will focus on the mechanics. Any suggestions?

Best regards,

Teng