Hi,<div><br /></div><div>Sorry for the delay in response here. I did add EI_SCALE14 and VDW_SCALE14 values, which I had not included before, however this does not change the ultimate outcome which is that NPT simulations with large numbers of constraints fail to converge to the correct box size for the system. Since I am only changing the number of constraints in my tests, I doubt that this issue has anything to do with the FF parameters/scaling. As I mentioned above, without constraints the box size contracts to 23A, while with 3 constraints (this being the only difference between my tests) it only contracts to 26.5A.</div><div><br /></div><div>Any further help/insight would be appreciated. </div><div><br /></div><div>Thanks,</div><div>Sean<br /></div><br /><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Wednesday, March 19, 2025 at 9:25:45 AM UTC-4 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">Hi Sean<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">Are you sure that the FF is set up properly, in particular, did you check if the values for
<a href="https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/MM/FORCEFIELD.html#CP2K_INPUT.FORCE_EVAL.MM.FORCEFIELD.EI_SCALE14" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/MM/FORCEFIELD.html%23CP2K_INPUT.FORCE_EVAL.MM.FORCEFIELD.EI_SCALE14&source=gmail&ust=1744916835344000&usg=AOvVaw1anNMbNs5P02-AjWrEmrBh">
EI_SCALE14</a> and <a href="https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/MM/FORCEFIELD.html#CP2K_INPUT.FORCE_EVAL.MM.FORCEFIELD.VDW_SCALE14" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/MM/FORCEFIELD.html%23CP2K_INPUT.FORCE_EVAL.MM.FORCEFIELD.VDW_SCALE14&source=gmail&ust=1744916835344000&usg=AOvVaw3OUZNpDLOYp5IowLCclfa3">
VDW_SCALE14</a> are correct?<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">Best<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></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><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-right:0cm;margin-bottom:12.0pt;margin-left:36.0pt">
<b><span style="color:black">From: </span></b><span style="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 Sean Larmore <<a href data-email-masked rel="nofollow">sean.l...@gmail.com</a>><br>
<b>Date: </b>Tuesday, 18 March 2025 at 21:48<br>
<b>To: </b>cp2k <<a href data-email-masked rel="nofollow">cp...@googlegroups.com</a>><br>
<b>Subject: </b>[CP2K:21297] NPT box size not reaching equilibrium with multiple atomic constraints<u></u><u></u></span></p>
</div>
<p class="MsoNormal" style="margin-left:36.0pt">Hi CP2K community, <u></u><u></u></p>
<div>
<p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt">I am trying to run an npt simulation on a molecule containing Boron with the generalized amber force field (GAFF). GAFF does not contain parameters for Boron, so I had set up these simulations to keep the Boron
atom (and it's connected bonds, angles, and dihedrals) constrained/frozen. However, I quickly noticed that the box size would not equilibrate and hovered around the initial box size, leading to significant void spaces in my solvent, poor solvent density, and
solvent distribution. <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt">I set up some control tests on a different molecule without Boron, so I knew the FF would not cause issues, and found that the issue seems to be caused by atomic constraints. As you can see in the attached graphs,
with no constraints the edge length of the box reaches an equilibrium value of ~23A, with one constraint it also goes to ~23A, with two constraints it goes to ~24.5A, and with three constraints it goes to ~26.5A (3.5A larger than the box without atomic constraints).
This essentially makes it impossible to have more than 1 or 2 constraints on a system as it goes through an npt, as the box size will never reach the correct equilibrium size. This also precludes me from my goal of simulating the boron containing molecule
I'm currently interested, as I need a minimum of 7 constraints. <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt">Does anyone have any insight into this problem with npt simulations and constraints and/or a potential work around in CP2K? I've also attached my input and output files for one of the constrained jobs. <br>
<br>
Thanks in advance,<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt">Sean<u></u><u></u></p>
</div>
</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">-- <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 data-email-masked rel="nofollow">cp2k+uns...@googlegroups.com</a>.<br>
To view this discussion visit <a href="https://groups.google.com/d/msgid/cp2k/6768d237-6879-45e0-985f-55a250183f41n%40googlegroups.com?utm_medium=email&utm_source=footer" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://groups.google.com/d/msgid/cp2k/6768d237-6879-45e0-985f-55a250183f41n%2540googlegroups.com?utm_medium%3Demail%26utm_source%3Dfooter&source=gmail&ust=1744916835345000&usg=AOvVaw1I9ZcGibA_InXr7DaLmBss">
https://groups.google.com/d/msgid/cp2k/6768d237-6879-45e0-985f-55a250183f41n%40googlegroups.com</a>.<u></u><u></u></p>
</div>
</div>
</div>
</div>
</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 visit <a href="https://groups.google.com/d/msgid/cp2k/ec6a686f-a952-4249-bb15-3459a7681b96n%40googlegroups.com?utm_medium=email&utm_source=footer">https://groups.google.com/d/msgid/cp2k/ec6a686f-a952-4249-bb15-3459a7681b96n%40googlegroups.com</a>.<br />