<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=windows-1253">
<style type="text/css" style="display:none;"> P {margin-top:0;margin-bottom:0;} </style>
</head>
<body dir="ltr">
<div class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="ContentPasted0">Dear Giovanni,</span></div>
<div class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="ContentPasted0"><br>
</span></div>
<div class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="ContentPasted0">Thank you for the resources, they're very helpful. I didn't know
that PLUMED can be used with newer versions of Quantum Espresso, I'll give it a try!</span></div>
<div class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="ContentPasted0"><br>
</span></div>
<div class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="ContentPasted0">Best regards,</span></div>
<div class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="ContentPasted0">Payal</span></div>
<div class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="ContentPasted0"><br>
</span></div>
<div class="elementToProof">
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div id="Signature">
<div>
<table style="border-collapse:collapse;border:none;width:auto;margin:0">
<tbody>
<tr>
<td valign="top" style="border:none;border-top:solid #D00000 2px;padding:18px"><img style="display:block" src="https://ucomm.unl.edu/images/email-signature/Nebraska_N_RGB_small_on_white.gif"></td>
<td valign="top" style="border:none;padding:15px 18px 18px 0;border-top:solid #D00000 2px">
<p style="margin:0px 2px 2px 2px;font-family:Helvetica, Arial;color:#454545;line-height:18px">
<strong>Payal Chaudhary</strong></p>
<p style="font-size:12px;margin:2px;font-style:italic;font-family:Georgia;color:#454545;line-height:14px">
Graduate Research Asst</p>
<p style="font-size:10px;margin:2px;font-family:Helvetica, Arial;color:#454545;line-height:14px">
University of Nebraska–Lincoln</p>
<p style="font-size:10px;margin:2px;font-family:Helvetica, Arial;color:#454545;line-height:14px">
Chemical & Biomolecular Engineering</p>
<p style="font-size:10px;margin:2px;font-family:Helvetica, Arial;color:#454545;line-height:14px">
212 Othmer Hall, Lincoln, NE 68588</p>
</td>
</tr>
</tbody>
</table>
</div>
</div>
</div>
<div id="appendonsend"></div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> users <users-bounces@lists.quantum-espresso.org> on behalf of Giovanni La Penna <giovanni.lapenna@cnr.it><br>
<b>Sent:</b> Tuesday, December 13, 2022 5:29 AM<br>
<b>To:</b> Quantum ESPRESSO users Forum <users@lists.quantum-espresso.org><br>
<b>Subject:</b> Re: [QE-users] Blue moon ensemble calculations in quantum espresso</font>
<div> </div>
</div>
<div class="BodyFragment"><font size="2"><span style="font-size:11pt;">
<div class="PlainText">Non-NU Email<br>
<br>
Payal,<br>
<br>
It is possible to use QE with PLUMED and then to apply PLUMED recipes:<br>
<br>
<a href="https://urldefense.com/v3/__https://www.plumed.org__;!!PvXuogZ4sRB2p-tU!E7oPJQZU_TGV_mHpRbnDdoLZWsSwIxm7GZoDAJtJssSLWr61cSCWylv2M5wcoLaCMCp3LxQ6hliIOgtUiYcFpu1Nsb9sZaD6B9R9$">https://urldefense.com/v3/__https://www.plumed.org__;!!PvXuogZ4sRB2p-tU!E7oPJQZU_TGV_mHpRbnDdoLZWsSwIxm7GZoDAJtJssSLWr61cSCWylv2M5wcoLaCMCp3LxQ6hliIOgtUiYcFpu1Nsb9sZaD6B9R9$</a>
<br>
<br>
Recently blue-moon sampling has been done with PLUMED combined together<br>
with other DFT codes:<br>
<br>
<a href="https://urldefense.com/v3/__https://doi.org/10.1007/s11244-021-01516-y__;!!PvXuogZ4sRB2p-tU!E7oPJQZU_TGV_mHpRbnDdoLZWsSwIxm7GZoDAJtJssSLWr61cSCWylv2M5wcoLaCMCp3LxQ6hliIOgtUiYcFpu1Nsb9sZT1t97kW$">https://urldefense.com/v3/__https://doi.org/10.1007/s11244-021-01516-y__;!!PvXuogZ4sRB2p-tU!E7oPJQZU_TGV_mHpRbnDdoLZWsSwIxm7GZoDAJtJssSLWr61cSCWylv2M5wcoLaCMCp3LxQ6hliIOgtUiYcFpu1Nsb9sZT1t97kW$</a>
<br>
<br>
The last time I used PLUMED 1.x in QE 5.2 (2016) to perform manipulations<br>
(not properly a correct sampling):<br>
<br>
<a href="https://urldefense.com/v3/__https://doi.org/10.3390/molecules23123308__;!!PvXuogZ4sRB2p-tU!E7oPJQZU_TGV_mHpRbnDdoLZWsSwIxm7GZoDAJtJssSLWr61cSCWylv2M5wcoLaCMCp3LxQ6hliIOgtUiYcFpu1Nsb9sZbQEGTUz$">https://urldefense.com/v3/__https://doi.org/10.3390/molecules23123308__;!!PvXuogZ4sRB2p-tU!E7oPJQZU_TGV_mHpRbnDdoLZWsSwIxm7GZoDAJtJssSLWr61cSCWylv2M5wcoLaCMCp3LxQ6hliIOgtUiYcFpu1Nsb9sZbQEGTUz$</a>
<br>
<br>
With a little handcraft, it is possible to use PW of QE 7.0 with PLUMED 2.7.x.<br>
Unfortunately not yet CP, as far as I know.<br>
<br>
HTH,<br>
Giovanni<br>
<br>
On Mon, Dec 12, 2022 at 09:59:48PM +0000, Payal Chaudhary wrote:<br>
> I had a question about running blue moon calculations with Quantum Espresso.<br>
> <br>
> 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_$
>)<br>
> <br>
> To calculate these averages, we need some quantities in the output file, such as the metric tensor z, and the Lagrange multiplier ë, for each time step. In the case of VASP, these can be obtained by specifying an additional input tag.<br>
> <br>
> 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.<br>
> I would really appreciate if someone could point me in the right direction to compute blue moon ensemble averages with the QE code.<br>
> <br>
_______________________________________________<br>
The Quantum ESPRESSO community stands by the Ukrainian<br>
people and expresses its concerns about the devastating<br>
effects that the Russian military offensive has on their<br>
country and on the free and peaceful scientific, cultural,<br>
and economic cooperation amongst peoples<br>
_______________________________________________<br>
Quantum ESPRESSO is supported by MaX (<a href=""></a>https://urldefense.com/v3/__http://www.max-centre.eu__;!!PvXuogZ4sRB2p-tU!E7oPJQZU_TGV_mHpRbnDdoLZWsSwIxm7GZoDAJtJssSLWr61cSCWylv2M5wcoLaCMCp3LxQ6hliIOgtUiYcFpu1Nsb9sZTsfDE33$ )<br>
users mailing list users@lists.quantum-espresso.org<br>
<a href="https://urldefense.com/v3/__https://lists.quantum-espresso.org/mailman/listinfo/users__;!!PvXuogZ4sRB2p-tU!E7oPJQZU_TGV_mHpRbnDdoLZWsSwIxm7GZoDAJtJssSLWr61cSCWylv2M5wcoLaCMCp3LxQ6hliIOgtUiYcFpu1Nsb9sZa6EQrEG$">https://urldefense.com/v3/__https://lists.quantum-espresso.org/mailman/listinfo/users__;!!PvXuogZ4sRB2p-tU!E7oPJQZU_TGV_mHpRbnDdoLZWsSwIxm7GZoDAJtJssSLWr61cSCWylv2M5wcoLaCMCp3LxQ6hliIOgtUiYcFpu1Nsb9sZa6EQrEG$</a>
<br>
</div>
</span></font></div>
</body>
</html>