[gmx-users] Qmmm (rose rahmani)

Groenhof, Gerrit ggroenh at gwdg.de
Sun Aug 5 21:33:43 CEST 2018


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



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
?is it recommended by GROMACS developers?

Best regards


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