[gmx-users] Qmmm (rose rahmani)

rose rahmani rose.rhmn93 at gmail.com
Sun Aug 5 21:50:34 CEST 2018


Thank you so mich for your derailed answer.

On Mon, 6 Aug 2018, 00:04 Groenhof, Gerrit, <ggroenh at gwdg.de> wrote:

> Hi,
>
> What is exactly your question?
>
> If it is whether you can use gromacs for QM/MM, the answer is yes.
>
> Whether your QM/MM model it is valid, is always up to you to check, as
> with any other pure QM, MM or QM/MM model. Sometimes, the validation for
> the model can be found in literature, sometimes you need to do a careful
> benchmark yourself.
>
> If for your systems,  DFTB is a valid model, then I can recommend using
> the DFTB implementation. If not, and you need ab initio or DFT  models,
> then you'd have to resort to a QM program that supports these methods for
> the QM engine in your QM/MM simulations. In that case, you can use the gau
> script from http://wwwuser.gwdg.de/~ggroenh/qmmm.html#gaussian

Is it free to use Gaussian?( as it's not free software generally)

>
> Gerrit
>
>
>
>
> Hi,
>
> I want to study the interaction of protein with functionalized
> nanotube(different fuctional groups) to know how protein can bind to
> functionalizedNT and calculate binding affinity,... . I want to try QMMM
> implemention in gromacs but as i'm beginner in such calculation methods(in
> gromacs), i wanna know am i right in using such method in GROMACS. Is ONIOM
> method and dft calculations just like quantum base softwares ( like
> Gaussian,...) ? I use to do MD simulations by GROMACS and results were
> always great but i have not tried QMMM. Is it as valid as quantum base
> calculation softwares?(sorry for being rude ;)))
> And how about this one
>
> http://cbp.cfn.kit.edu/joomla/index.php/downloads/18-gromacs-with-qm-mm-using-dftb3
> ?is
> <http://cbp.cfn.kit.edu/joomla/index.php/downloads/18-gromacs-with-qm-mm-using-dftb3?is>
> it recommended by GROMACS developers?
>
> Best regards
> Rose
>
>
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