Thank you Gustavo and Marc for your reply,
So I'll do the QM/MM calculation by AmberTools and because I want to do the MD run by GROMACS I have to convert it to GROMACS format. Is it ok to do it in AmberTools then convert the files to GROMACS?
Mohammad.
On Wednesday, April 6, 2016 2:01 AM, Marc van der Kamp <marcvanderkamp.gmail.com> wrote:
Just a quick addition/correction to Gustavo's answers:
In most/all common implementations of hybrid QM/MM calculations using the additive approach, including in sander, the vdW interaction between QM and MM regions is modelled using an MM force field term (typically Lennard-Jones). The Force-field (atom type) of the QM atoms *does* thus affect the QM/MM calculation.
Marc
Sent from my iPhone
> On 5 Apr 2016, at 09:06 pm, Gustavo Seabra <gustavo.seabra.gmail.com> wrote:
>
> 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 Fri Apr 08 2016 - 02:30:03 PDT
