CCL: Combined Molecular Dynamics and Semiempirical Methods

 Sent to CCL by: "Ross Walker" [ross .. rosswalker.co.uk]
 Dear Heribert,
 > I'm looking for a way to do a classical molecular dynamics simulation
 > of a liquid (ideally with a polarizable Force Field), but with one
 > molecule treated by semiempirical methods (PM3 or similar), so
 > basically a QM/MM calculation. I know that there is the GAMESS-Tinker
 > combination, but it seems that it does not allow to compute
 > trajectories (also the version of Tinker used seems to be a bit old).
 >
 > Anyone knows a possibility to do this? A bit of additional
 > programming
 > would not be an unsurmountable hurdle.
 Amber 9 has full support for QM/MM MD simulations that can combine a number
 of different semi-empirical Hamiltonians with any of the Amber force fields.
 It also supports a full treatment of long range electrostatics using a
 Particle Mesh Ewald approach for the QM/MM calculation and also supports
 QM/MM with Generalized Born implicit solvent. The implementation is also
 very simple so that if you have a simulation setup to run classically in
 Amber already you only need to change a couple of entires in your input file
 and you are good to go.
 Details on amber are at http://amber.scripps.edu
 A tutorial on AMBER 9 QM/MM is at
 http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_Six_amber9/ind
 ex.htm
 All the best
 Ross
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 |\oss Walker
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 | San Diego Supercomputer Center |
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