P.S. These calculations were done based of the input files in https://www.cp2k.org/exercises:2018_uzh_acpc2:mol_sol, 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.<div><br /></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Monday 22 January 2024 at 14:03:06 UTC+1 Léon Luntadila Lufungula 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;">Dear Matthias,<div><br></div><div>I have similar results for a box of 256 water molecules:</div><div>NVT:</div><div><img alt="NVT-256.png" width="596px" height="432px" src="https://groups.google.com/group/cp2k/attach/721f9288cda1e/NVT-256.png?part=0.1&view=1"><br>NPT: (fluctuations are a bit smaller but still in the range of several kbar...)</div><div><img alt="NPT-256.png" width="596px" height="432px" src="https://groups.google.com/group/cp2k/attach/721f9288cda1e/NPT-256.png?part=0.3&view=1"><img alt="Pressure-256.png" width="592px" height="432px" src="https://groups.google.com/group/cp2k/attach/721f9288cda1e/Pressure-256.png?part=0.2&view=1"><br></div><div><br></div><div><span style="font-size:14.6667px">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...</span><br></div><div><span style="font-size:14.6667px"><br></span></div><div><span style="font-size:14.6667px">Kind regards,</span></div><div><span style="font-size:14.6667px">Léon</span></div><div><br></div><div><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Monday 22 January 2024 at 13:40:05 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>
<p class="MsoNormal"><span lang="DE-CH" style="font-size:11.0pt">Dear Léon<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="DE-CH" style="font-size:11.0pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><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
<a href="https://github.com/cp2k/cp2k/blob/master/tests/Fist/regtest-water/H2O-TIP3P-6x6x6.inp" rel="nofollow" target="_blank" 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=1706014990446000&usg=AOvVaw0kYwZ0RRyP3jynWIWNBBCb">
input</a>. The sample should be equilibrated well in advance before starting the sampling run.<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">HTH<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">Matthias<u></u><u></u></span></p>
<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 rel="nofollow">cp...@googlegroups.com</a> <<a rel="nofollow">cp...@googlegroups.com</a>> on behalf of Léon Luntadila Lufungula <<a rel="nofollow">Leon.luntad...@uantwerpen.be</a>><br>
<b>Date: </b>Monday, 22 January 2024 at 12:56<br>
<b>To: </b>cp2k <<a rel="nofollow">cp...@googlegroups.com</a>><br>
<b>Subject: </b>[CP2K:19784] 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">Dear all,<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">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:36.0pt"><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:36.0pt"><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:36.0pt"><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: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">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:36.0pt"><span style="font-size:11.0pt">NVE:<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>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><img border="0" width="605" height="432" style="width:6.302in;min-height:4.5in" src="https://groups.google.com/group/cp2k/attach/720b7b929b503/NVE.png?part=0.1&view=1"><u></u><u></u></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">NVT:<u></u><u></u></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><img border="0" width="613" height="432" style="width:6.3854in;min-height:4.5in" src="https://groups.google.com/group/cp2k/attach/720b7b929b503/NVT.png?part=0.4&view=1"><u></u><u></u></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">NPT:<u></u><u></u></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><img border="0" width="613" height="432" style="width:6.3854in;min-height:4.5in" src="https://groups.google.com/group/cp2k/attach/720b7b929b503/NPT.png?part=0.3&view=1"><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>
<p class="MsoNormal" style="margin-left:36.0pt"><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: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">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" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en-GB&q=https://groups.google.com/g/cp2k/c/gxA8r6wmyF4/m/k8QT7iglAAAJ&source=gmail&ust=1706014990447000&usg=AOvVaw14s8yi9-mQ-ksk23PyFnYO">
another post</a>, but that person did not get a reply unfortunately....<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>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><img border="0" width="600" height="432" style="width:6.25in;min-height:4.5in" src="https://groups.google.com/group/cp2k/attach/720b7b929b503/Pressure.png?part=0.2&view=1"><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>
<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">Thanks in advance for the help!<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-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><p class="MsoNormal" style="margin-left:36.0pt"><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
<a rel="nofollow">cp2k+uns...@googlegroups.com</a>.<br>
To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/76d3e94b-4a67-4fcc-8861-78a566ebb107n%40googlegroups.com?utm_medium=email&utm_source=footer" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en-GB&q=https://groups.google.com/d/msgid/cp2k/76d3e94b-4a67-4fcc-8861-78a566ebb107n%2540googlegroups.com?utm_medium%3Demail%26utm_source%3Dfooter&source=gmail&ust=1706014990447000&usg=AOvVaw2Z4LZHYvB9BKl1CR2RarT1">
https://groups.google.com/d/msgid/cp2k/76d3e94b-4a67-4fcc-8861-78a566ebb107n%40googlegroups.com</a>.<u></u><u></u></span></p>
</div>
</div>
</div>
</div>
</blockquote></div></blockquote></div>
<p></p>
-- <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 <a href="mailto:cp2k+unsubscribe@googlegroups.com">cp2k+unsubscribe@googlegroups.com</a>.<br />
To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/e6d4002e-91a7-45cd-817c-adc66616d1d6n%40googlegroups.com?utm_medium=email&utm_source=footer">https://groups.google.com/d/msgid/cp2k/e6d4002e-91a7-45cd-817c-adc66616d1d6n%40googlegroups.com</a>.<br />