Hi ...<div><br /></div><div>How did you find this syntax for the input?</div><div><br /></div><div>Such a constraint is defined through the use of collective variables in the section SUBSYS.</div><div>Then the CONSTRAINT section is as follows</div><div><p style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal; color: rgb(0, 0, 0);"><span style="font-variant-ligatures: no-common-ligatures;">&MOTION</span></p>
<p style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal; color: rgb(255, 255, 255); background-color: rgb(203, 0, 206);"><span style="font-variant-ligatures: no-common-ligatures; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);"> &</span><span style="font-variant-ligatures: no-common-ligatures;">CONSTRA</span><span style="font-variant-ligatures: no-common-ligatures; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">INT</span></p>
<p style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal; color: rgb(0, 0, 0);"><span style="font-variant-ligatures: no-common-ligatures;"> &COLLECTIVE</span></p>
<p style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal; color: rgb(0, 0, 0);"><span style="font-variant-ligatures: no-common-ligatures;"> COLVAR 1</span></p>
<p style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal; color: rgb(0, 0, 0);"><span style="font-variant-ligatures: no-common-ligatures;"> MOLECULE 1</span></p>
<p style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal; color: rgb(0, 0, 0);"><span style="font-variant-ligatures: no-common-ligatures;"> TARGET 1.9275</span></p>
<p style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal; color: rgb(0, 0, 0);"><span style="font-variant-ligatures: no-common-ligatures;"> &END COLLECTIVE</span></p><p style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal; color: rgb(0, 0, 0);"><span style="font-variant-ligatures: no-common-ligatures;"><br /></span></p><p style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal; color: rgb(0, 0, 0);">.....</p><p style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal; color: rgb(0, 0, 0);"><br /></p><p style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal; color: rgb(0, 0, 0);">The Shake and Rattle algorithm is used to enforce it. </p><p style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal; color: rgb(0, 0, 0);"><br /></p><p style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal; color: rgb(0, 0, 0);">Regards</p><br /></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Thursday, March 6, 2025 at 4:11:23 PM UTC+1 Planck 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;"><p>I am trying to run a CP2K molecular dynamics simulation where specific bond lengths should remain fixed. Based on the documentation, SHAKE should be used, but I keep encountering errors when defining it under &CONSTRAINT or &MD.</p><p>Here is my attempt:</p><div><div>```</div><div><div><div><span aria-label="Copy">Copy</span>Edit</div></div></div><div dir="ltr">&MOTION
<br> &CONSTRAINT
<br> &SHAKE<br> ATOMS 1 2<br> TYPE BOND
<br> &END SHAKE
<br> &END CONSTRAINT
<br>&END MOTION<br>```</div></div><p>However, CP2K returns an error:</p><div><div><br></div><div dir="ltr">``` unknown subsection SHAKE of section CONSTRAINT```</div></div><p>I also tried defining SHAKE within &MD, but CP2K does not recognize that either.</p><p>What is the correct way to fix bond lengths using SHAKE in CP2K? If SHAKE is not supported in the latest versions, what alternative approach should I use?</p><p>Thank you for any suggestion and help</p></blockquote></div>
<p></p>
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