Re: basis set for QM-MM dft

From: Marcelo C. R. Melo (melomcr_at_gmail.com)
Date: Wed Jan 25 2017 - 13:18:36 CST

Hello,

That seems to have escaped your attention. The isn't any keyword or option
for that because NAMD has no influence over the method (B3LYP, HF, PM7,
etc) or basis set chosen for a given simulation. Our documentation for
QM/MM in NAMD does not try to cover every functionality offered by ORCA
and/or MOPAC, nor will it ever try to. We do provide a way to send your
multiple configuration lines to ORCA (and single configuration line to
MOPAC) through NAMD by using the "qmConfigLine" keyword. If the
functionality requires more extensive manipulations of the ORCA input file,
you could use the "custom" quantum chemistry software interface, and the
tcl script provided in the example in our website, to execute advanced
manipulations of your input.

If you are looking for a way to use different basis sets, you should go
directly to ORCA's manual (https://orcaforum.cec.mpg.de/OrcaManual.pdf) and
check what is required of your input file.

For something as simple as changing the basis set for an element, a quick
look in the manual shows you that one additional line in your NAMD
configuration script would be enough:

qmConfigLine "%%basis newgto C \"6-31G*\" end end"

Best,
Marcelo

---
Marcelo Cardoso dos Reis Melo
PhD Candidate
Luthey-Schulten Group
University of Illinois at Urbana-Champaign
crdsdsr2_at_illinois.edu
+1 (217) 244-5983 <(217)%20244-5983>
On 25 January 2017 at 09:15, Francesco Pietra <chiendarret_at_gmail.com> wrote:
> Hello:
>
> Unless it has escaped my attention there is no way with NAMD12-ORCA to set
> different basis set for different elements of the QM part. It is a common
> procedure (and need) with DFT calculations using a higher basis set for
> transition elements than for protein H, C, N, O, S. Will that come with
> more detailed notes?
>
> thanks
>
> francesco pietra
>
---
Marcelo Cardoso dos Reis Melo
PhD Candidate
Luthey-Schulten Group
University of Illinois at Urbana-Champaign
crdsdsr2_at_illinois.edu
+1 (217) 244-5983
On 25 January 2017 at 09:15, Francesco Pietra <chiendarret_at_gmail.com> wrote:
> Hello:
>
> Unless it has escaped my attention there is no way with NAMD12-ORCA to set
> different basis set for different elements of the QM part. It is a common
> procedure (and need) with DFT calculations using a higher basis set for
> transition elements than for protein H, C, N, O, S. Will that come with
> more detailed notes?
>
> thanks
>
> francesco pietra
>

This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:21:01 CST