Re: [AMBER] Using DFT-D3(BJ) during QM/MM calculations

From: Zhiyi Wu <>
Date: Tue, 2 Mar 2021 20:12:32 +0000

Hi Andy,
Kind regards,
Zhiyi Wu

> On 2 Mar 2021, at 20:05, Goetz, Andreas <> wrote:
> Hi Zhiyi,
> The dispersion between QM and MM regions is handled by the classical force field (LJ potential). All interactions between atoms within the QM region are entirely handled by the QM method. If you ask for BLYP you will get BLYP without dispersion corrections.
> If you use a density functional that includes (empirical) dispersion corrections, then you can pass it just via the method parameter in the &gau namelist, for example method = ‘B97D3’. In all other cases you will have to use a template input file with name gau_job.tpl. File content should be as follows for BLYP-D3BJ/def2SVP:
> mdin:
> &gau
> use_template = 1,
> /
> gau_job.tpl:
> #P BLYP/def2SVP EmpiricalDispersion=GD3BJ
> All the best,
> Andy
> —
> Dr. Andreas W. Goetz
> Assistant Research Scientist
> San Diego Supercomputer Center
> Tel: +1-858-822-4771
> Email:
> Web:
>> On Mar 2, 2021, at 2:22 AM, Zhiyi Wu <> wrote:
>> Dear Amber user,
>> I’m interested in using Amber/Gaussian to do QM/MM calculations at the level BLYP/Def2SVP. When using Gaussian, I usually need to add DFT-D3(BJ) dispersion correction to account for the dispersion interactions.
>> I wonder if I would still need DFT-D3(BJ) during QM/MM calculation? The dispersion between the QM region and the MM region or between the atoms in the MM region is taken into account by Lennard-Jones potential.
>> Is the dispersion between the atoms in the QM region taken into account by the Lennard-Jones potential as well, or one would need to add dispersion correction via DFT-D3(BJ)?
>> I noticed that the keyword to add dispersion interactions is not included in the amber/Gaussian interface so I assume that it is not needed but I’m not too sure about that.
>> Kind regards,
>> Zhiyi Wu
>> _______________________________________________
>> AMBER mailing list
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Tue Mar 02 2021 - 12:30:03 PST
Custom Search