Hi Mohammad,
Just to clarify a couple of things:
> Does MM simulation depend on the force field which I used?
Yes. MM uses the force field to calculate the energy function and derivatives needed for the dynamics.
> Because QM calculation depends on the force field which I used
No. A pure QM calculation should *NOT* depend, in any way, on the force field parameters. Unless you are talking about a hybrid QM/MM calculation in which case the energy of the QM region still does not depend on the force field used (except for the charges that polarize the QM region). The only really FF-dependent terms would be the terms that cross the QM-MM boundaries.
> and according to that I used amber force field I asked it here. Indeed I was thinking that amber tools can do it for me.
You can certainly do MM, QM and QM/MM simulations with AmberTools, there is no need to converto to GROMACS, unless there is some special requirement on your system.
Best,
Gustavo.
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Received on Tue Apr 05 2016 - 13:30:04 PDT
