Hi Matthias,<div><br /></div><div>So I started an NpT directly from the inputs you gave me with a box containing 216 water molecules. After a 300ps equilibration (plots thus starrt at 0.3 ns), the pressure fluctuations are again in the 10kbar range which is okay as you pointed out, while the average pressure is around -14 bar, so tha'ts also within the 20 bar range you mentioned. The energy drift per atom is also below 1K so everything seems to work reasonably. </div><div><br /></div><div><img alt="H2O-TIP3P_FLEXIBLE-6x6x6.mp-NPT-plots.png" width="1076px" height="1292px" src="cid:dac9197f-4388-4dcc-bd2a-ecdcaa1651a3" /><br />I'm starting my AIMD simulations as we speak, so hopefully all goes well there too. I read that it is best to do a short equilibration with a strong coupling to the thermostat (e.g. CSVR, TIMECON 20 and REGION MASSIVE), before going to a weaker coupling (e.g. CSVR, TIMECON 200 and REGION GLOBAL), but is there also a rule of thumb w.r.t. the barostat TIMECON? I regularly see TIMECON 1000, but is it useful to set it to TIMECON 100 in this early equilibration?</div><div><br /></div><div>Thanks for all the help already, it really helps me a lot given the fact that I don't have a senior researcher with a lot of hands-on CP2K experience around!</div><div><br /></div><div>Kind regards,</div><div>Léon</div><div><br /></div><div><br /></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Monday 22 January 2024 at 17:09:26 UTC+1 Krack Matthias wrote:<br/></div><blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"> <div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"> <div> <ol style="margin-top:0cm" start="1" type="1"> <li style="margin-left:0cm"><span lang="DE-CH" style="font-size:11.0pt">Yes, if possible<u></u><u></u></span></li><li style="margin-left:0cm"><span lang="EN-US" style="font-size:11.0pt">The average pressure wrt the desired target pressure however should be in the order of +/- 20 bar<u></u><u></u></span></li><li style="margin-left:0cm"><span lang="EN-US" style="font-size:11.0pt">You can start directly with NpT. I would add “RESTART_COUNTERS no” to “RESTART_AVERAGES no”.<u></u><u></u></span></li></ol> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"><u></u> <u></u></span></p> <div> <div></div></div></div></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><div><div><div> <div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0cm 0cm 0cm"> <p class="MsoNormal" style="margin-right:0cm;margin-bottom:12.0pt;margin-left:36.0pt"> <b><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">From: </span></b><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black"><a href data-email-masked rel="nofollow">cp...@googlegroups.com</a> <<a href data-email-masked rel="nofollow">cp...@googlegroups.com</a>> on behalf of Léon Luntadila Lufungula <<a href data-email-masked rel="nofollow">Leon.luntad...@uantwerpen.be</a>><br> <b>Date: </b>Monday, 22 January 2024 at 16:53<br> <b>To: </b>cp2k <<a href data-email-masked rel="nofollow">cp...@googlegroups.com</a>><br> <b>Subject: </b>Re: [CP2K:19795] Cons. Qty for different ensembles + Pressure fluctuation<u></u><u></u></span></p> </div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Hi Matthias,<u></u><u></u></span></p> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><u></u> <u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">1) Okay, I'll keep an eye on the "Energy drift per atom [K]"-values then for my AIMD simulations, I'm guessing for an equilibrated structure these should be near or below 1K? <u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">2) That's a relief that fluctuations in the order of kbar are normal, I was getting worried about what to do to get them in the order of bar!<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">3) I'll make sure to set RESTART_AVERAGES to NO when restarting my NPT from my NVT, or is it actually not necessary to first do an NVT before running NPT?<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><u></u> <u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Kind regards,<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-right:0cm;margin-bottom:12.0pt;margin-left:36.0pt"> <span style="font-size:11.0pt">Léon<u></u><u></u></span></p> </div> </div></div></div></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><div><div><div><div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">On Monday 22 January 2024 at 16:02:20 UTC+1 Krack Matthias wrote:<u></u><u></u></span></p> </div> </div></div></div></div></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><div><div><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm"> <div> <div> <p class="MsoNormal" style="margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">Hi Léon</span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">Indeed, the </span><span style="font-size:11.0pt">"Energy drift per atom [K]" </span><span lang="EN-US" style="font-size:11.0pt">provides a good indicator for checking the equilibration. Given the small cell sizes used in atomistic simulations, pressure fluctuation up to a kbar range are normal, because a mHa/Bohr^3 corresponds to roughly 294 kbar. The pressure usually equilibrates much more slowly than the temperature. On restart, with RESTART_AVERAGES NO, the averages should evolve smoothly and should not change too much for an equilibrated system.</span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">Best</span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">Matthias</span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><u></u><u></u></span></p> </div> </div> </blockquote></div></div></div></div></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><div><div><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm"><div><div><div><div> <div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0cm 0cm 0cm"> <p class="MsoNormal" style="margin-bottom:12.0pt;margin-left:72.0pt"> <b><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">From: </span></b><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black"><span><a href data-email-masked rel="nofollow">cp...@googlegroups.com</a></span> <<span><a href data-email-masked rel="nofollow">cp...@googlegroups.com</a></span>> on behalf of Léon Luntadila Lufungula <<span><a href data-email-masked rel="nofollow">Leon.luntad...@uantwerpen.be</a></span>><br> <b>Date: </b>Monday, 22 January 2024 at 15:07<br> <b>To: </b>cp2k <<span><a href data-email-masked rel="nofollow">cp...@googlegroups.com</a></span>><br> <b>Subject: </b>Re: [CP2K:19792] Cons. Qty for different ensembles + Pressure fluctuation</span><span style="font-size:11.0pt"><u></u><u></u></span></p> </div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt">Hi Jurg and Matthias,<u></u><u></u></span></p> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt"> <u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt">Jurg:<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt">1) Okay, good to know that I can reduce the fluctuations by increasing the system size. Still, are fluctuations in the order of kbar not too large when the desired pressure is 1 bar?<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt">2) I'm using the CSVR thermostat with a timecon of 100 fs and the barostat is the standard one with a timecon of 100 fs by just including the following lines to the input and changing the ensemble to NPT_I: <u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt">&BAROSTAT<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt"> TIMECON 100<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt">&END BAROSTAT<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt">2-continued) I do see now that the BAROSTAT section also has a THERMOSTAT subsection. Should the thermostat be defined here in the case of an NPT calculation or is it in the THERMOSTAT subsection of MD as is the case for an NVT run? If not, what is the use of the BAROSTAT/THERMOSTAT subsection?<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt"> <u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt">Matthias:<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt">Thanks for pointing this out to me! I remembered noticing that the value for GMAX was too small this weekend, but I forgot to adjust it accordingly. I'll try to re-run the calculations with the inputs in the regtest-water directory to see if I get better results! Maybe one more question if that's okay for you. I'm also running / getting ready to run AIMD simulations and these are quite heavy so it takes a long time to simulate even a couple of ps. If I see a drift in the constant of motion like in the pictures above, is there a way of knowing if this is due to an error in the input or just because the system has not equilibrated yet? Or is this just a matter of simulating for longer and longer times to see if it goes towards an equilibrium or keeps drifting? Perhaps the "Energy drift per atom [K]" in the output can be of some help, but I'm not certain how it's calculated or how I can use it to check my trajectory...<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt"> <u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt">Thanks for all the help!<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt"> <u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt">Kind regards,<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt">Léon<u></u><u></u></span></p> </div> </div></div></div></div></blockquote></div></div></div></div></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><div><div><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm"><div><div><div><div><div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt">On Monday 22 January 2024 at 14:29:09 UTC+1 Krack Matthias wrote:<u></u><u></u></span></p> </div> </div></div></div></div></div></blockquote></div></div></div></div></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><div><div><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm"><div><div><div><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"> <div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span lang="EN-US" style="font-size:11.0pt">Hi</span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:72.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:72.0pt"> <span lang="EN-US" style="font-size:11.0pt">The GMAX parameter for Ewald is a bit sloppy in these inputs. Suggested values are 1 to 2 points per Angstrom based on the cell edge lengths, i.e. GMAX 20 is numerically more appropriate. In the example I gave you the GMAX value is automatically adapted to the cell size.</span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:72.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:72.0pt"> <span lang="EN-US" style="font-size:11.0pt">Best</span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:72.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:72.0pt"> <span lang="EN-US" style="font-size:11.0pt">Matthias</span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:72.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><u></u><u></u></span></p> </div> </div> <div> <div> <div> <div> <div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0cm 0cm 0cm"> <p class="MsoNormal" style="margin-bottom:12.0pt;margin-left:108.0pt"> <b><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">From: </span></b><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black"><span><a href data-email-masked rel="nofollow">cp...@googlegroups.com</a></span> <<span><a href data-email-masked rel="nofollow">cp...@googlegroups.com</a></span>> on behalf of Léon Luntadila Lufungula <<span><a href data-email-masked rel="nofollow">Leon.luntad...@uantwerpen.be</a></span>><br> <b>Date: </b>Monday, 22 January 2024 at 14:13<br> <b>To: </b>cp2k <<span><a href data-email-masked rel="nofollow">cp...@googlegroups.com</a></span>><br> <b>Subject: </b>Re: [CP2K:19788] Cons. Qty for different ensembles + Pressure fluctuation</span><span style="font-size:11.0pt"><u></u><u></u></span></p> </div> <p class="MsoNormal" style="margin-left:108.0pt"> <span style="font-size:11.0pt">P.S. These calculations were done based of the input files in <a href="https://www.cp2k.org/exercises:2018_uzh_acpc2:mol_sol" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en-GB&q=https://www.cp2k.org/exercises:2018_uzh_acpc2:mol_sol&source=gmail&ust=1706088631314000&usg=AOvVaw3gcjXuSxROcDE_68yYgdje">https://www.cp2k.org/exercises:2018_uzh_acpc2:mol_sol</a>, because the Fist regtest-water folder was not yet available at the time, but the FF params are correct, the coordinates are just different than the one molecule box in the tests directory.<u></u><u></u></span></p> <div> <p class="MsoNormal" style="margin-left:108.0pt"> <span style="font-size:11.0pt"> <u></u><u></u></span></p> </div> </div> </div> </div> </div> <div> <div> <div> <div> <div> <div> <p class="MsoNormal" style="margin-left:108.0pt"> <span style="font-size:11.0pt">On Monday 22 January 2024 at 14:03:06 UTC+1 Léon Luntadila Lufungula wrote:<u></u><u></u></span></p> </div> </div> </div> </div> </div> </div> <div> <div> <div> <div> <div> <blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"> <p class="MsoNormal" style="margin-left:108.0pt"> <span style="font-size:11.0pt">Dear Matthias,<u></u><u></u></span></p> <div> <p class="MsoNormal" style="margin-left:108.0pt"> <span style="font-size:11.0pt"> <u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:108.0pt"> <span style="font-size:11.0pt">I have similar results for a box of 256 water molecules:<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:108.0pt"> <span style="font-size:11.0pt">NVT:<u></u><u></u></span></p> </div> </blockquote> </div> </div> </div> </div> </div> </blockquote></div></div></div></div></div></blockquote></div></div></div></div></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><div><div><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm"><div><div><div><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"><div> <div> <div> <div> <div> <blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"> <div> <p class="MsoNormal" style="margin-left:108.0pt"> <span style="font-size:11.0pt;border:solid windowtext 1.0pt;padding:0cm"><img border="0" width="32" height="32" style="width:.3333in;min-height:.3333in" alt="Image removed by sender."></span><span style="font-size:11.0pt"><u></u><u></u></span></p> </div> </blockquote> </div> </div> </div> </div> </div></blockquote></div></div></div></div></div></blockquote></div></div></div></div></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><div><div><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm"><div><div><div><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"> <div> <div> <div> <div> <div> <blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"> <div> <p class="MsoNormal" style="margin-left:108.0pt"> <span style="font-size:11.0pt"><br> NPT: (fluctuations are a bit smaller but still in the range of several kbar...)<u></u><u></u></span></p> </div> </blockquote> </div> </div> </div> </div> </div> </blockquote></div></div></div></div></div></blockquote></div></div></div></div></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><div><div><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm"><div><div><div><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"><div> <div> <div> <div> <div> <blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"> <div> <p class="MsoNormal" style="margin-left:108.0pt"> <span style="font-size:11.0pt;border:solid windowtext 1.0pt;padding:0cm"><img border="0" width="32" height="32" style="width:.3333in;min-height:.3333in" alt="Image removed by sender."><img border="0" width="32" height="32" style="width:.3333in;min-height:.3333in" alt="Image removed by sender."></span><span style="font-size:11.0pt"><u></u><u></u></span></p> </div> </blockquote> </div> </div> </div> </div> </div> <div> <div> <div> <div> <div> <blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"></blockquote></div></div></div></div></div></blockquote></div></div></div></div></div></blockquote></div></div></div></div></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><div><div><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm"><div><div><div><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"><div><div><div><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"> <div> <p class="MsoNormal" style="margin-left:108.0pt"> <span style="font-size:11.0pt"> <u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:108.0pt"> <span style="font-size:11.0pt">You say that the sample should be equilibrated well in advance before starting the sampling run, so do you mean I should run an NVT simulation for longer until it equilibrates before running an NPT from the thermalized end structure? Or do you mean both NVT and NPT should be run for longer until the Cons. Qty. is also equilibrated? Because in both cases the temperature seems to be equilibrated quite well and the pressure in the NPT ensemble is also constant albeit with very large oscillations...<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:108.0pt"> <span style="font-size:11.0pt"> <u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:108.0pt"> <span style="font-size:11.0pt">Kind regards,<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:108.0pt"> <span style="font-size:11.0pt">Léon<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:108.0pt"> <span style="font-size:11.0pt"> <u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:108.0pt"> <span style="font-size:11.0pt"> <u></u><u></u></span></p> </div> </blockquote></div></div></div></div></div></blockquote></div></div></div></div></div></blockquote></div></div></div></div></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><div><div><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm"><div><div><div><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"><div><div><div><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"><div> <div> <p class="MsoNormal" style="margin-left:108.0pt"> <span style="font-size:11.0pt">On Monday 22 January 2024 at 13:40:05 UTC+1 Krack Matthias wrote:<u></u><u></u></span></p> </div> </div></blockquote></div></div></div></div></div></blockquote></div></div></div></div></div></blockquote></div></div></div></div></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><div><div><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm"><div><div><div><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"><div><div><div><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"> <div> <div> <p class="MsoNormal" style="margin-left:108.0pt"> <span lang="EN-US" style="font-size:11.0pt">Dear Léon</span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:108.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:108.0pt"> <span lang="EN-US" style="font-size:11.0pt">a 32 H2O cell is still a relatively small system which can cause large fluctuations. I suggest to try at least the 6x6x6 = 216 H2O </span><span style="font-size:11.0pt"><a href="https://github.com/cp2k/cp2k/blob/master/tests/Fist/regtest-water/H2O-TIP3P-6x6x6.inp" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en-GB&q=https://github.com/cp2k/cp2k/blob/master/tests/Fist/regtest-water/H2O-TIP3P-6x6x6.inp&source=gmail&ust=1706088631314000&usg=AOvVaw2WYYQtryHUun1TeRCkCA6Z"><span lang="EN-US">input</span></a></span><span lang="EN-US" style="font-size:11.0pt">. The sample should be equilibrated well in advance before starting the sampling run.</span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:108.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:108.0pt"> <span lang="EN-US" style="font-size:11.0pt">HTH</span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:108.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:108.0pt"> <span lang="EN-US" style="font-size:11.0pt">Matthias</span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:108.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><u></u><u></u></span></p> </div> </div> <div> <div> <div> <div> <div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0cm 0cm 0cm"> <p class="MsoNormal" style="margin-bottom:12.0pt;margin-left:144.0pt"> <b><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">From: </span></b><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black"><span><a href data-email-masked rel="nofollow">cp...@googlegroups.com</a></span> <<span><a href data-email-masked rel="nofollow">cp...@googlegroups.com</a></span>> on behalf of Léon Luntadila Lufungula <<span><a href data-email-masked rel="nofollow">Leon.luntad...@uantwerpen.be</a></span>><br> <b>Date: </b>Monday, 22 January 2024 at 12:56<br> <b>To: </b>cp2k <<span><a href data-email-masked rel="nofollow">cp...@googlegroups.com</a></span>><br> <b>Subject: </b>[CP2K:19784] Cons. Qty for different ensembles + Pressure fluctuation</span><span style="font-size:11.0pt"><u></u><u></u></span></p> </div> <p class="MsoNormal" style="margin-left:144.0pt"> <span style="font-size:11.0pt">Dear all,<u></u><u></u></span></p> <div> <p class="MsoNormal" style="margin-left:144.0pt"> <span style="font-size:11.0pt"> <u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:144.0pt"> <span style="font-size:11.0pt">I ran several simulations on a box of 32 water molecules with the TIP3P force field:<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:144.0pt"> <span style="font-size:11.0pt">1) 1 ns NVE trajectory with timestep 0.5 fs<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:144.0pt"> <span style="font-size:11.0pt">2) 1 ns NVT trajectory at 298.15K with timestep 0.5 fs and thermostat time constant of 100fs<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:144.0pt"> <span style="font-size:11.0pt"> 3) 1 ns NPT_I trajectory restarted from the final structure of the NVT trajectory at 298.15K and 1 bar with timestep 0.5 and thermostat and barostat time constants of 100 fs<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:144.0pt"> <span style="font-size:11.0pt"> <u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:144.0pt"> <span style="font-size:11.0pt">I plotted the Cons. Qty [a.u.] vs. Time [fs] for the three simulations and saw that the constant of motion was only more or less constant for the NVE trajectory. The NVT and NPT trajectories both had strong oscillations and significant drift of the constant of motion (see below) and I was wondering if this is normal behaviour or that this means that the system is not yet equilibrated? I would think that the Cons. Qty. should remain constant but I can also understand that the thermostat and barostat might influence its behaviour in a way.<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:144.0pt"> <span style="font-size:11.0pt">NVE:<u></u><u></u></span></p> </div> </div> </div> </div> </div> </blockquote></div></blockquote></div></div></div></div></div></blockquote></div></div></div></div></div></blockquote></div></div></div></div></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><div><div><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm"><div><div><div><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"><div><div><div><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"><div> <div> <div> <div> <div> <p class="MsoNormal" style="margin-left:144.0pt"> <span style="font-size:11.0pt;border:solid windowtext 1.0pt;padding:0cm"><img border="0" width="605" height="432" style="width:6.302in;min-height:4.5in" alt="Image removed by sender."></span><span style="font-size:11.0pt"><u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:144.0pt"> <span style="font-size:11.0pt">NVT:<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:144.0pt"> <span style="font-size:11.0pt;border:solid windowtext 1.0pt;padding:0cm"><img border="0" width="613" height="432" style="width:6.3854in;min-height:4.5in" alt="Image removed by sender."></span><span style="font-size:11.0pt"><u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:144.0pt"> <span style="font-size:11.0pt">NPT:<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:144.0pt"> <span style="font-size:11.0pt;border:solid windowtext 1.0pt;padding:0cm"><img border="0" width="613" height="432" style="width:6.3854in;min-height:4.5in" alt="Image removed by sender."></span><span style="font-size:11.0pt"><u></u><u></u></span></p> </div> </div> </div> </div> </div></blockquote></div></blockquote></div></div></div></div></div></blockquote></div></div></div></div></div></blockquote></div></div></div></div></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><div><div><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm"><div><div><div><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"><div><div><div><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"> <div> <div> <div> <div> <div> <p class="MsoNormal" style="margin-left:144.0pt"> <span style="font-size:11.0pt">The simulations of the water box were small test cases, but I also need to know what behaviour to expect when going to my production runs with my systems of interest...<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:144.0pt"> <span style="font-size:11.0pt"> <u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:144.0pt"> <span style="font-size:11.0pt">Additionally, in the NPT ensemble, the pressure seems to fluctuate very strongly from -20000 to +20000 bar which seems to be quite excessive to me. Is this normal? I've also seen this asked in <a href="https://groups.google.com/g/cp2k/c/gxA8r6wmyF4/m/k8QT7iglAAAJ" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en-GB&q=https://groups.google.com/g/cp2k/c/gxA8r6wmyF4/m/k8QT7iglAAAJ&source=gmail&ust=1706088631314000&usg=AOvVaw0lli1ts5ldg7vpFc-MrlMn"> another post</a>, but that person did not get a reply unfortunately....<u></u><u></u></span></p> </div> </div> </div> </div> </div> </blockquote></div></blockquote></div></div></div></div></div></blockquote></div></div></div></div></div></blockquote></div></div></div></div></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><div><div><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm"><div><div><div><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"><div><div><div><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"><div> <div> <div> <div> <div> <p class="MsoNormal" style="margin-left:144.0pt"> <span style="font-size:11.0pt;border:solid windowtext 1.0pt;padding:0cm"><img border="0" width="600" height="432" style="width:6.25in;min-height:4.5in" alt="Image removed by sender."></span><span style="font-size:11.0pt"><u></u><u></u></span></p> </div> </div> </div> </div> </div></blockquote></div></blockquote></div></div></div></div></div></blockquote></div></div></div></div></div></blockquote></div></div></div></div></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><div><div><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm"><div><div><div><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"><div><div><div><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"> <div> <div> <div> <div> <div> <p class="MsoNormal" style="margin-left:144.0pt"> <span style="font-size:11.0pt"> <u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:144.0pt"> <span style="font-size:11.0pt">Thanks in advance for the help!<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:144.0pt"> <span style="font-size:11.0pt"> <u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:144.0pt"> <span style="font-size:11.0pt">Kind regards,<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:144.0pt"> <span style="font-size:11.0pt">Léon<u></u><u></u></span></p> </div> </div> </div> </div> </div> <div> <div> <div> <div> <p class="MsoNormal" style="margin-left:144.0pt"> <span style="font-size:11.0pt">-- <br> You received this message because you are subscribed to the Google Groups "cp2k" group.<br> To unsubscribe from this group and stop receiving emails from it, send an email to <span><a href data-email-masked rel="nofollow">cp2k+uns...@googlegroups.com</a></span>.<br> To view this discussion on the web visit <a 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