From owner-chemistry@ccl.net Sun Apr 2 08:00:00 2023 From: "Andras P. Borosy borosy{}bluewin.ch" To: CCL Subject: CCL: Best force field and computer application for protein and DNA MD simulations? Message-Id: <-54882-230401183326-14847-aUq3PdAMWpPjxoUrVqSE9w() server.ccl.net> X-Original-From: "Andras P. Borosy" Content-Language: en-US Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Sun, 2 Apr 2023 00:33:15 +0200 MIME-Version: 1.0 Sent to CCL by: "Andras P. Borosy" [borosy(_)bluewin.ch] Dear Colleagues, What is the best force field and computer application for MD simulations of the interaction of small proteins with DNA or RNA? I mean best the highest quality, most reliable. Speed is not very important for me now. Best wishes, Andras Borosy From owner-chemistry@ccl.net Sun Apr 2 11:50:01 2023 From: "Cheng Fei Phung feiphung ~~ hotmail.com" To: CCL Subject: CCL: accurate computation for active and inactive orbitals Message-Id: <-54883-230402114845-16628-xpAcpMC5XycubwQc4AChTg###server.ccl.net> X-Original-From: Cheng Fei Phung Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_SEYPR06MB5514FC22C2F45B51E981C7DAC18D9SEYPR06MB5514apcp_" Date: Sun, 2 Apr 2023 15:48:21 +0000 MIME-Version: 1.0 Sent to CCL by: Cheng Fei Phung [feiphung-#-hotmail.com] --_000_SEYPR06MB5514FC22C2F45B51E981C7DAC18D9SEYPR06MB5514apcp_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi Susi Lehtola, > From https://pyscf.org/user/ci.html#frozen-orbitals , it still requires the= exact list of the orbital indices (which is the question of this thread). ``` # freeze 2 core orbitals myci =3D ci.CISD(mf, frozen=3D[0,1]).run() # freeze 2 core orbitals and 3 unoccupied orbitals myci =3D ci.CISD(mf, frozen=3D[0,1,16,17,18]).run() ``` Could you tell us more about the use of Improved Virtual orbitals in this p= articular context ? Regards, Phung Cheng Fei ________________________________ > From: owner-chemistry+feiphung=3D=3Dhotmail.com(!)ccl.net on behalf of Susi Lehtola susi.lehtola() a= lumni.helsinki.fi Sent: Friday, March 31, 2023 10:47 PM To: Phung, Cheng Fei Subject: CCL: accurate computation for active and inactive orbitals Sent to CCL by: Susi Lehtola [susi.lehtola-$-alumni.helsinki.fi] On 3/31/23 07:47, Cheng Fei Phung feiphung-,-hotmail.com wrote: > > Sent to CCL by: "Cheng Fei Phung" [feiphung#hotmail.com] > Could anyone provide accurate computation for active and inactive orbital= s to be used in https://qiskit.org/documentation/nature/locale/bn_BN/stubs/= qiskit_nature.second_q.transformers.FreezeCoreTransformer.html and > https://qiskit.org/documentation/nature/stubs/qiskit_nature.second_q.tran= sformers.ActiveSpaceTransformer.html ? > > My current inaccurate solution is using HOMO-LUMO approach. See https://= github.com/tencent-quantum-lab/tensorcircuit/issues/120#issuecomment-145793= 2770 > > I am looking at https://www.scm.com/doc/BAND/index.html which seems to pr= ovide [some DFT methods](https://i.imgur.com/mHeWCtl.png) to do so. > > However, I do not have access to SCM software. > > Any suggestions ? There is a common misunderstanding here by what is meant by 1) active and inactive orbitals in many-electron calculations, 2) the selection of the ac= tive space orbitals, and 3) the use of a frozen core in ADF. 1. the active and inactive orbitals in many-electron calculations refer to whether substitutions from/to the orbital is allowed when building the many-electron basis, similarly to the complete active space (CAS) method wh= ich is what quantum simulators are approximating. One builds the Hamiltonian an= d diagonalizes it in the space of active orbitals, only. 2. the choice of the active space orbitals is a complicated issue, mostly because of limitations of classical computers. Unoccupied orbitals of Hartree-Fock theory are often a bad starting point due to the incorrect for= m of the potential experienced by the virtual orbitals in Hartree-Fock theory. M= any alternatives have been suggested in the literature, ranging from Improved Virtual Orbitals to the use of natural orbitals from a lower level of theor= y, such as M=F8ller-Plesset perturbation theory truncated at the second order = (MP2) or configuration interaction singles and doubles (CISD). The latter class o= f methods is available in PySCF, for example, for which Qiskit has an interfa= ce; see the PySCF documentation for how to build the density matrices and natur= al orbitals. 3. the frozen core orbitals in ADF refer to their behavior in self-consiste= nt field (SCF) calculations, meaning here Hartree-Fock and density functional theory. Since the core orbitals are much lower in energy, polarization effe= cts in a chemical environment are smaller for them than for the valence orbital= s, which is the foundation for freezing the core orbitals to the atomic form. = This is also the foundation for the pseudopotential and effective core potential approaches. Susi -- ---------------------------------------------------------------------------= --- Mr. Susi Lehtola, PhD Academy of Finland research fellow susi.lehtola[*]helsinki.fi Associate professor, computational chem= istry http://susilehtola.github.io/ University of Helsinki, Finland ---------------------------------------------------------------------------= --- Susi Lehtola, FT akatemiatutkija susi.lehtola[*]helsinki.fi dosentti, laskennallinen kemia http://susilehtola.github.io/ Helsingin yliopisto ---------------------------------------------------------------------------= --- -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--_000_SEYPR06MB5514FC22C2F45B51E981C7DAC18D9SEYPR06MB5514apcp_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi Susi Lehtola,

> From https://pyscf.org/user/ci.html#frozen-orbitals , it still requi= res the exact list of the orbital indices (which is the question of this th= read).

```
# freeze 2 core orbitals=0A=
myci =3D ci.CISD(=
mf, frozen=3D[0,1]).run()=0A=
# freeze 2 core orbitals and 3 unoccupied=
 orbitals=0A=
myci =3D ci.CISD(=
mf, frozen=3D[0,1,16,17,18]).run()
```

Could you tell us more about the use of Improved Virtual orbitals in this p= articular context ?

Regards,
Phung Cheng Fei
From: owner-chemistry+feiph= ung=3D=3Dhotmail.com(!)ccl.net <owner-chemistry+feiphung=3D=3Dhotmail.com(!)= ccl.net> on behalf of Susi Lehtola susi.lehtola() alumni.helsinki.fi <owner-chemistry(!)ccl.net>
Sent: Friday, March 31, 2023 10:47 PM
To: Phung, Cheng Fei <feiphung(!)hotmail.com>
Subject: CCL: accurate computation for active and inactive orbitals<= /font>
 

Sent to CCL by: Susi Lehtola [susi.lehtola-$-alumni.helsinki.fi]
On 3/31/23 07:47, Cheng Fei Phung feiphung-,-hotmail.com wrote:
>
> Sent to CCL by: "Cheng Fei  Phung" [feiphung#hotmail.co= m]
> Could anyone provide accurate computation for active and inactive orbi= tals to be used in https://qiskit.org/documentation/nature/locale/bn_BN/stubs/qiskit_nature.se= cond_q.transformers.FreezeCoreTransformer.html and
> https://qiskit.org/documentation/nature/stubs/qiskit_nature.second_q.transf= ormers.ActiveSpaceTransformer.html ?
>
> My current inaccurate solution is using HOMO-LUMO approach.  See = https://github.com/tencent-quantum-lab/tensorcircuit/issues/120#issuecommen= t-1457932770
>
> I am looking at ht= tps://www.scm.com/doc/BAND/index.html which seems to provide [some DFT = methods](https://i.imgur.com/mH= eWCtl.png) to do so.
>
> However, I do not have access to SCM software.
>
> Any suggestions ?

There is a common misunderstanding here by what is meant by 1) active and inactive orbitals in many-electron calculations, 2) the selection of the ac= tive
space orbitals, and 3) the use of a frozen core in ADF.

1. the active and inactive orbitals in many-electron calculations refer to<= br> whether substitutions from/to the orbital is allowed when building the
many-electron basis, similarly to the complete active space (CAS) method wh= ich
is what quantum simulators are approximating. One builds the Hamiltonian an= d
diagonalizes it in the space of active orbitals, only.

2. the choice of the active space orbitals is a complicated issue, mostly because of limitations of classical computers. Unoccupied orbitals of
Hartree-Fock theory are often a bad starting point due to the incorrect for= m of
the potential experienced by the virtual orbitals in Hartree-Fock theory. M= any
alternatives have been suggested in the literature, ranging from Improved Virtual Orbitals to the use of natural orbitals from a lower level of theor= y,
such as M=F8ller-Plesset perturbation theory truncated at the second order = (MP2)
or configuration interaction singles and doubles (CISD). The latter class o= f
methods is available in PySCF, for example, for which Qiskit has an interfa= ce;
see the PySCF documentation for how to build the density matrices and natur= al
orbitals.

3. the frozen core orbitals in ADF refer to their behavior in self-consiste= nt
field (SCF) calculations, meaning here Hartree-Fock and density functional<= br> theory. Since the core orbitals are much lower in energy, polarization effe= cts
in a chemical environment are smaller for them than for the valence orbital= s,
which is the foundation for freezing the core orbitals to the atomic form. = This
is also the foundation for the pseudopotential and effective core potential=
approaches.

Susi
--
---------------------------------------------------------------------------= ---
Mr. Susi Lehtola, PhD         =     Academy of Finland research fellow
susi.lehtola[*]helsinki.fi        &= nbsp; Associate professor, computational chemistry
http://susilehtola.github.io/=      University of Helsinki, Finland
---------------------------------------------------------------------------= ---
Susi Lehtola, FT          = ;        akatemiatutkija
susi.lehtola[*]helsinki.fi        &= nbsp; dosentti, laskennallinen kemia
http://susilehtola.github.io/=      Helsingin yliopisto
---------------------------------------------------------------------------= ---



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