[gmx-users] Qm/mm

Alex nedomacho at gmail.com
Sun Aug 26 08:31:42 CEST 2018

ORCA has a googlable manual. ;)

If your nanotube-protein interaction is not mediated by water and the 
protein (or its region of interest) is not larger than, say, 100 atoms, 
you could also try CP2K, which allows doing DFT and forcefield-based 
calculations, so you could pass structures back and forth between the 
methods. For one, CP2K is pretty fast, though I am not sure 32 gigs or 
RAM would be enough for DFT-level calculations of hundreds of atoms. 
Depends on the level of theory, of course, but ab initio and DFT scale 
with system size _very_ differently from forcefield-based MD.


On 8/25/2018 11:48 PM, rose rahmani wrote:
> Hi Albert,
> I want to study the interaction of functionalized inorganic nanotube with
> protein. I just can use free software. Is ORCA ok for my needs? I don't
> know anything about it.i couldn't use some softwares like Gaussian and
> quantum espresso because Gaussian is commercial and Quantum Espresso is not
> Ok for nanotube with more than 100 atoms...
> Is ORCA suitable for these systems?[ Does it need special computers(high
> processing)? I use computer (linux)with RAM 32GB]
> If yes, would you please introduce me some valuable sites and tutorials for
> Best
> Rose
> On Sat, 25 Aug 2018, 18:18 Albert, <mailmd2011 at gmail.com> wrote:
>> why not try some professional QM/MM software like "ORCA". It will make
>> your life much easier.
>> On 08/24/2018 11:54 PM, rose rahmani wrote:
>>> Hi,
>>> I want to use qm/mm calculations(dfb3 code & ONIOM method) in gromacs.
>>> Since, some of these codes are commercial(like ONIOM specially
>> Gaussian), i
>>> wanted to ask are these all free in GROMACS? Or we should first register
>>> and by these codes separately and then use them in GROMACS?
>>> Best regards
>>> Rose
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