[gmx-users] QM/MM simulation

Mostafa Javaheri javaheri.gromacs at gmail.com
Sat Aug 26 17:17:18 CEST 2017

 Dear gmx users
I'm doing an QM/MM simulation of a ligand-protein system by the Gromacs
ORCA interface. When I set constraint = none in the Gromacs mdp file the
bonds' length of the atoms oscillate extremely even those that did not
index as the QM atoms e.g. aromatic rings will be twisted during the mdrun
and when I set constraint = all-bonds I get this error “Step 1, time 0.002
(ps) LINCS WARNING relative constraint deviation after LINCS” I thinks this
happens because I constrained the reactant atoms explicitly in the topology
file. Are these kind of oscillations usual in QM/MM simulations?
Note When I set QMMM = No in the mdp file no unusual vibration happens. Any
help will be appreciated.

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