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QM/MM: CPMD/GROMOS<br />
• Hamiltonian yiels consistent Euler-‐Lagrange equa4ons for energy-conserving<br />
MD propaga4on <br />
• QM: CPMD plane wave/pseudopoten4al Kohn-‐Sham representa4on <br />
• MM: GROMOS simula4on package (including par4cle-‐par4cle/par4cle-mesh<br />
(P 3 M) algorithm <br />
• Electrosta4c embedding tailored to study dynamics of complex <br />
biomolecular systems and chemical reac4ons. <br />
• Hierarchical approach to deal with electrosta4c interac4ons in <br />
combina4on with an empirical modifica4on of the short-‐range terms <br />
that does not require a refit of the MM force field used. <br />
QM −MM<br />
E nb<br />
QM −MM QM −MM<br />
= E es<br />
+ E steric<br />
n(r)<br />
= ∑ q I ∫<br />
r − R I<br />
dr + ∑ ∑ υ vdW<br />
R a<br />
− R I<br />
I ∈MM<br />
I ∈MM α ∈QM<br />
( )<br />
• QM system must be treated as a finite cluster by decoupling it from the <br />
ar4ficial periodic images (e.g. Martyna-‐Tuckerman decoupling) <br />
A. Laio, J. VandeVondele, U. Röthlisberger J. Chem. Phys. 2002, 116, 6941.
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