Hi James,
See brief answers below.
1) What the information from the initial ff parameters of my QM group taken
> from the prmtop would be most meaningful for the qm/mm simulation.
> Previously you've mentioned that this information will be ignored during
> qm/mm run but it seem that initial molecular 3D geometry and charge
> distribution have some matter, haven't it?
>
> As mentioned before, only the MM parameters of QM atoms should matter.
Of course, the coordinates (3D geometry) matter too.
MM force-field charges will be ignored (as will the bonded MM terms) for
the QM atoms.
> 2) What are the most reasonable methods and tools for the analysis of QM/MM
> trajectories ? On what dynamical properties of simulated system should I
> paid most of attention? E.g the most trivial is the analysis of the 3D
> geometry during simulation. How can I make such analysis obtaining both
> visualization and numerical values (E.g torsion angles in
> functional-relevant groups)? Does it possible to calculate charge density
> for those groups as well?
>
> What you want/need to analyze depends on your system/your questions; tools
etc. are the same as used for pure MM.
This thread (about QM/MM) is not the right place to go into this. First
check the available manual (e.g. of ptraj & cpptraj) and tutorials.
If you want to get the position of link atoms, you need to use the writepdb
option in the sander input file, see manual for details.
You can print Mulliken charges of the QM atoms to get an idea about the
'charge density' (see under sqm in the AmberTools manual).
Hope this helps,
Marc
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Received on Mon May 19 2014 - 05:30:02 PDT
