There are many plans for new features, but not as many people realizing
those plans ... meta-dynamics together with first-principle MD is
computationally heavy and I am not sure that there is a lot of interest
for it, so I do not expect that it will be available soon
Paolo
On 14/12/2022 18:37, Payal Chaudhary wrote:
Dear Paolo,
Thanks for letting me know. Just asking for future reference, are there
any plans to add support for it again in the future, or to include
meta-dynamics within the QE code itself?
Thanks and regards,
Payal
*Payal Chaudhary*
Graduate Research Asst
University of Nebraska–Lincoln
Chemical & Biomolecular Engineering
212 Othmer Hall, Lincoln, NE 68588
------------------------------------------------------------------------
*From:* Paolo Giannozzi <[email protected]>
*Sent:* Wednesday, December 14, 2022 2:58 AM
*To:* Payal Chaudhary <[email protected]>
*Subject:* Re: [QE-users] [SPAM] Re: Blue moon ensemble calculations in
quantum espresso
Non-NU Email
On 12/14/22 00:54, Payal Chaudhary wrote:
Thank you for the resources, they're very helpful. I didn't know that
PLUMED can be used with newer versions of Quantum Espresso
unfortunately it can't. Support for the old version (v.1.3) of PLUMED
has been present for a long time but it was recently removed.
Paolo
Payal
*Payal Chaudhary*
Graduate Research Asst
University of Nebraska–Lincoln
Chemical & Biomolecular Engineering
212 Othmer Hall, Lincoln, NE 68588
------------------------------------------------------------------------
*From:* users <[email protected]> on behalf of
Giovanni La Penna <[email protected]>
*Sent:* Tuesday, December 13, 2022 5:29 AM
*To:* Quantum ESPRESSO users Forum <[email protected]>
*Subject:* Re: [QE-users] Blue moon ensemble calculations in quantum
espresso
Non-NU Email
Payal,
It is possible to use QE with PLUMED and then to apply PLUMED recipes:
https://urldefense.com/v3/__https://www.plumed.org__;!!PvXuogZ4sRB2p-tU!E7oPJQZU_TGV_mHpRbnDdoLZWsSwIxm7GZoDAJtJssSLWr61cSCWylv2M5wcoLaCMCp3LxQ6hliIOgtUiYcFpu1Nsb9sZaD6B9R9$
<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fwww.plumed.org__%3B!!PvXuogZ4sRB2p-tU!E7oPJQZU_TGV_mHpRbnDdoLZWsSwIxm7GZoDAJtJssSLWr61cSCWylv2M5wcoLaCMCp3LxQ6hliIOgtUiYcFpu1Nsb9sZaD6B9R9%24&data=05%7C01%7Cpaolo.giannozzi%40uniud.it%7Cb1001b10cee04460686a08daddf9d7b0%7C6e6ade15296c4224ac581c8ec2fd53a8%7C0%7C0%7C638066362532820640%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ei83MY79ET1YjWx3bTXAXlU%2BIX7pXc9MFsbJi1tU2bA%3D&reserved=0>
<https://urldefense.com/v3/__https://eur01.safelinks.protection.outlook.com/?url=https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fwww.plumed.org__*3B!!PvXuogZ4sRB2p-tU!E7oPJQZU_TGV_mHpRbnDdoLZWsSwIxm7GZoDAJtJssSLWr61cSCWylv2M5wcoLaCMCp3LxQ6hliIOgtUiYcFpu1Nsb9sZaD6B9R9*24&data=05*7C01*7Cpaolo.giannozzi*40uniud.it*7C2818eb7c95d04c0e589808dadd657cb5*7C6e6ade15296c4224ac581c8ec2fd53a8*7C0*7C0*7C638065725221086498*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000*7C*7C*7C&sdata=plS7R*2BhPY79AJkWW651eO8CDSVlg60MLn8a8kRf2bKM*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!PvXuogZ4sRB2p-tU!FAjJY45qkL4_ja5Vp4nbGqDI-a0iPLxeCHPcL-t-BNU_9Y90tlPlbPYPnmZ7McpN_2D9ZQ_rHEoBK9j30pX_b6LPNfB29zMFrjAK7g$
>
Recently blue-moon sampling has been done with PLUMED combined together
with other DFT codes:
https://urldefense.com/v3/__https://doi.org/10.1007/s11244-021-01516-y__;!!PvXuogZ4sRB2p-tU!E7oPJQZU_TGV_mHpRbnDdoLZWsSwIxm7GZoDAJtJssSLWr61cSCWylv2M5wcoLaCMCp3LxQ6hliIOgtUiYcFpu1Nsb9sZT1t97kW$
<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fdoi.org%2F10.1007%2Fs11244-021-01516-y__%3B!!PvXuogZ4sRB2p-tU!E7oPJQZU_TGV_mHpRbnDdoLZWsSwIxm7GZoDAJtJssSLWr61cSCWylv2M5wcoLaCMCp3LxQ6hliIOgtUiYcFpu1Nsb9sZT1t97kW%24&data=05%7C01%7Cpaolo.giannozzi%40uniud.it%7Cb1001b10cee04460686a08daddf9d7b0%7C6e6ade15296c4224ac581c8ec2fd53a8%7C0%7C0%7C638066362532820640%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Mu4omi3lLI6IsqgUUsxcFp3uXvdwkln1L3wh8YGGhn4%3D&reserved=0>
<https://urldefense.com/v3/__https://eur01.safelinks.protection.outlook.com/?url=https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fdoi.org*2F10.1007*2Fs11244-021-01516-y__*3B!!PvXuogZ4sRB2p-tU!E7oPJQZU_TGV_mHpRbnDdoLZWsSwIxm7GZoDAJtJssSLWr61cSCWylv2M5wcoLaCMCp3LxQ6hliIOgtUiYcFpu1Nsb9sZT1t97kW*24&data=05*7C01*7Cpaolo.giannozzi*40uniud.it*7C2818eb7c95d04c0e589808dadd657cb5*7C6e6ade15296c4224ac581c8ec2fd53a8*7C0*7C0*7C638065725221086498*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000*7C*7C*7C&sdata=tlOvtHSuWGkUd*2BaQXLzCCNTtATDIYsw*2FA4PDBvqpF5o*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!PvXuogZ4sRB2p-tU!FAjJY45qkL4_ja5Vp4nbGqDI-a0iPLxeCHPcL-t-BNU_9Y90tlPlbPYPnmZ7McpN_2D9ZQ_rHEoBK9j30pX_b6LPNfB29zP3lar9KA$
>
The last time I used PLUMED 1.x in QE 5.2 (2016) to perform manipulations
(not properly a correct sampling):
https://urldefense.com/v3/__https://doi.org/10.3390/molecules23123308__;!!PvXuogZ4sRB2p-tU!E7oPJQZU_TGV_mHpRbnDdoLZWsSwIxm7GZoDAJtJssSLWr61cSCWylv2M5wcoLaCMCp3LxQ6hliIOgtUiYcFpu1Nsb9sZbQEGTUz$
<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fdoi.org%2F10.3390%2Fmolecules23123308__%3B!!PvXuogZ4sRB2p-tU!E7oPJQZU_TGV_mHpRbnDdoLZWsSwIxm7GZoDAJtJssSLWr61cSCWylv2M5wcoLaCMCp3LxQ6hliIOgtUiYcFpu1Nsb9sZbQEGTUz%24&data=05%7C01%7Cpaolo.giannozzi%40uniud.it%7Cb1001b10cee04460686a08daddf9d7b0%7C6e6ade15296c4224ac581c8ec2fd53a8%7C0%7C0%7C638066362532820640%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=F3PYBXblcSyvzFdfftRjvvo2LRN%2F48buARqsPxYjqZw%3D&reserved=0>
<https://urldefense.com/v3/__https://eur01.safelinks.protection.outlook.com/?url=https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fdoi.org*2F10.3390*2Fmolecules23123308__*3B!!PvXuogZ4sRB2p-tU!E7oPJQZU_TGV_mHpRbnDdoLZWsSwIxm7GZoDAJtJssSLWr61cSCWylv2M5wcoLaCMCp3LxQ6hliIOgtUiYcFpu1Nsb9sZbQEGTUz*24&data=05*7C01*7Cpaolo.giannozzi*40uniud.it*7C2818eb7c95d04c0e589808dadd657cb5*7C6e6ade15296c4224ac581c8ec2fd53a8*7C0*7C0*7C638065725221086498*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000*7C*7C*7C&sdata=W2M71JqvtY2Fj1amsbYkZXs8Lh30SAaUyfHwmRIxzxA*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJQ!!PvXuogZ4sRB2p-tU!FAjJY45qkL4_ja5Vp4nbGqDI-a0iPLxeCHPcL-t-BNU_9Y90tlPlbPYPnmZ7McpN_2D9ZQ_rHEoBK9j30pX_b6LPNfB29zOvsKK3sg$
>
With a little handcraft, it is possible to use PW of QE 7.0 with PLUMED
2.7.x.
Unfortunately not yet CP, as far as I know.
HTH,
Giovanni
On Mon, Dec 12, 2022 at 09:59:48PM +0000, Payal Chaudhary wrote:
I had a question about running blue moon calculations with Quantum Espresso.
To get the free energy profile along a reaction coordinate, we can run several
constrained MD calculations and use the blue moon ensemble averages to get free energy
gradients. These gradients can then be integrated to get the free energy profile. This
methodology is described in the paper "Giovanni Ciccotti & Mauro Ferrario (2004)
Blue Moon Approach to Rare Events, Molecular Simulation, 30:11-12,
787-793"
(doi<https://urldefense.com/v3/__https://doi.org/10.1080/0892702042000270214__;!!PvXuogZ4sRB2p-tU!E7oPJQZU_TGV_mHpRbnDdoLZWsSwIxm7GZoDAJtJssSLWr61cSCWylv2M5wcoLaCMCp3LxQ6hliIOgtUiYcFpu1Nsb9sZasMlba_$ >)
To calculate these averages, we need some quantities in the output file, such
as the metric tensor z, and the Lagrange multiplier λ, for each time step. In
the case of VASP, these can be obtained by specifying an additional input tag.
The QE docs are not clear on whether these quantities are printed in the
output, and I couldn't find any discussion on this in the forums either.
I would really appreciate if someone could point me in the right direction to
compute blue moon ensemble averages with the QE code.
_______________________________________________
The Quantum ESPRESSO community stands by the Ukrainian
people and expresses its concerns about the devastating
effects that the Russian military offensive has on their
country and on the free and peaceful scientific, cultural,
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_______________________________________________
Quantum ESPRESSO is supported by MaX
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<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Flists.quantum-espresso.org%2Fmailman%2Flistinfo%2Fusers__%3B!!PvXuogZ4sRB2p-tU!E7oPJQZU_TGV_mHpRbnDdoLZWsSwIxm7GZoDAJtJssSLWr61cSCWylv2M5wcoLaCMCp3LxQ6hliIOgtUiYcFpu1Nsb9sZa6EQrEG%24&data=05%7C01%7Cpaolo.giannozzi%40uniud.it%7Cb1001b10cee04460686a08daddf9d7b0%7C6e6ade15296c4224ac581c8ec2fd53a8%7C0%7C0%7C638066362532820640%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=qlh2oivw0hHBYbbnLMN4jTZiBQDtTYw7P23zCqdxe4Y%3D&reserved=0>
<https://urldefense.com/v3/__https://eur01.safelinks.protection.outlook.com/?url=https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Flists.quantum-espresso.org*2Fmailman*2Flistinfo*2Fusers__*3B!!PvXuogZ4sRB2p-tU!E7oPJQZU_TGV_mHpRbnDdoLZWsSwIxm7GZoDAJtJssSLWr61cSCWylv2M5wcoLaCMCp3LxQ6hliIOgtUiYcFpu1Nsb9sZa6EQrEG*24&data=05*7C01*7Cpaolo.giannozzi*40uniud.it*7C2818eb7c95d04c0e589808dadd657cb5*7C6e6ade15296c4224ac581c8ec2fd53a8*7C0*7C0*7C638065725221086498*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000*7C*7C*7C&sdata=HH6euzLEZWGsvfqrCknh*2F8KWiXzbtc46xdbGoSY0IHQ*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!PvXuogZ4sRB2p-tU!FAjJY45qkL4_ja5Vp4nbGqDI-a0iPLxeCHPcL-t-BNU_9Y90tlPlbPYPnmZ7McpN_2D9ZQ_rHEoBK9j30pX_b6LPNfB29zN01kX-_A$
>
_______________________________________________
The Quantum ESPRESSO community stands by the Ukrainian
people and expresses its concerns about the devastating
effects that the Russian military offensive has on their
country and on the free and peaceful scientific, cultural,
and economic cooperation amongst peoples
_______________________________________________
Quantum ESPRESSO is supported by MaX
(https://urldefense.com/v3/__http://www.max-centre.eu__;!!PvXuogZ4sRB2p-tU!FAjJY45qkL4_ja5Vp4nbGqDI-a0iPLxeCHPcL-t-BNU_9Y90tlPlbPYPnmZ7McpN_2D9ZQ_rHEoBK9j30pX_b6LPNfB29zPPkq679w$
)
users mailing list [email protected]
https://urldefense.com/v3/__https://lists.quantum-espresso.org/mailman/listinfo/users__;!!PvXuogZ4sRB2p-tU!FAjJY45qkL4_ja5Vp4nbGqDI-a0iPLxeCHPcL-t-BNU_9Y90tlPlbPYPnmZ7McpN_2D9ZQ_rHEoBK9j30pX_b6LPNfB29zNRCLQxwQ$
<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Flists.quantum-espresso.org%2Fmailman%2Flistinfo%2Fusers__%3B!!PvXuogZ4sRB2p-tU!FAjJY45qkL4_ja5Vp4nbGqDI-a0iPLxeCHPcL-t-BNU_9Y90tlPlbPYPnmZ7McpN_2D9ZQ_rHEoBK9j30pX_b6LPNfB29zNRCLQxwQ%24&data=05%7C01%7Cpaolo.giannozzi%40uniud.it%7Cb1001b10cee04460686a08daddf9d7b0%7C6e6ade15296c4224ac581c8ec2fd53a8%7C0%7C0%7C638066362532820640%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Tdc1uhDvklGyyzzaVbZyv1Yw02RmSLvFV2xc2gDDuio%3D&reserved=0>
--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216
_______________________________________________
The Quantum ESPRESSO community stands by the Ukrainian
people and expresses its concerns about the devastating
effects that the Russian military offensive has on their
country and on the free and peaceful scientific, cultural,
and economic cooperation amongst peoples
_______________________________________________
Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
users mailing list [email protected]
https://lists.quantum-espresso.org/mailman/listinfo/users
