<div dir="ltr">Hi Azade,<div><br></div><div>Thanks for your answer. The molname is defined in the PSF file, in the topology section. The molname seems to be identified correctly as it is present in the output file (attached) in the description of the topology.</div><div><br></div><div>Regards,</div><div>Pierre</div><div><br>On Wednesday, June 17, 2020 at 12:20:32 PM UTC+1, Azade Yazdan Yar wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div dir="ltr"><div style="font-family:arial,helvetica,sans-serif;color:#000000">Hi Pierre, </div><div style="font-family:arial,helvetica,sans-serif;color:#000000">I know some of the answers to your first question. </div><div style="font-family:arial,helvetica,sans-serif;color:#000000">What you use in the ATOMS should be the index of atoms within that molecule. Constraints will be applied to all molecules with the same MOLNAME or MOLECULE number. </div><div style="font-family:arial,helvetica,sans-serif;color:#000000">From your input file, I cannot see how the <span style="font-family:Arial,Helvetica,sans-serif;color:rgb(34,34,34)">SWM4 molecules are defined in the coordinates section. You have to define the MOLNAME in that part as below (what I have as H2O, or MOLECULE 1). Note that if you use MOLECULE, it is the '</span><em style="font-family:Arial,Helvetica,sans-serif;color:rgb(34,34,34)">molecule <b>kind</b> number' </em><span style="font-family:Arial,Helvetica,sans-serif;color:rgb(34,34,34)">and not molecule number.</span></div><div style="font-family:arial,helvetica,sans-serif;color:#000000"><span style="font-family:Arial,Helvetica,sans-serif;color:rgb(34,34,34)"><br></span></div><div style="font-family:arial,helvetica,sans-serif;color:#000000"><span style="font-family:Arial,Helvetica,sans-serif;color:rgb(34,34,34)">Hope this helps,</span></div><div style="font-family:arial,helvetica,sans-serif;color:#000000"><span style="font-family:Arial,Helvetica,sans-serif;color:rgb(34,34,34)">Azade</span></div><div style="font-family:arial,helvetica,sans-serif;color:#000000"><br></div><div style="font-family:arial,helvetica,sans-serif;color:#000000">&G3X3<br></div><div style="font-family:arial,helvetica,sans-serif;color:#000000"> MOLECULE 1<br> ATOMS 1..3<br> DISTANCES a b c<br> &END G3X3<br></div><div style="font-family:arial,helvetica,sans-serif;color:#000000"><br></div><div style="font-family:arial,helvetica,sans-serif;color:#000000">O 5.1692824047308950E+00 5.3185376653354242E+00 2.1483827179189252E+01 H2O 1<br></div></div><br><div class="gmail_quote"><div dir="ltr">On Wed, Jun 17, 2020 at 12:41 PM Pierre-André Cazade <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="eUY9EwU6BwAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">pie...@gmail.com</a><wbr>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Dear CP2K users,<div><br></div><div>I am trying to use G3X3 constraints on my water molecules during a CELL_OPT motion. Needless to say, that it does not work. The "manual" is not very clear about the indexes that need to be provided. Should I use the index of the atoms in the coordinate file, for example 15761 15762 15763, or the indexes within the water molecule itself: 1 2 3. Does such constraint apply to all my water molecules provided they have the same molname "SWM4" or do I need an entry for each water molecule?</div><div><br></div><div>What about VIRTUAL_SITES?</div><div><br></div><div>Finally, the "CONTRAINT_INFO ON" section does not print a single information in the output to help me out.</div><div><br></div><div>I attached my input file for clarity.</div><div><br></div><div>Regards,</div><div>Pierre</div><div><br></div><div><br></div></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="javascript:" target="_blank" gdf-obfuscated-mailto="eUY9EwU6BwAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">cp...@googlegroups.<wbr>com</a>.<br> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/0a1b04bc-ad4c-4cd0-babc-7f694e836288o%40googlegroups.com?utm_medium=email&utm_source=footer" target="_blank" rel="nofollow" onmousedown="this.href='https://groups.google.com/d/msgid/cp2k/0a1b04bc-ad4c-4cd0-babc-7f694e836288o%40googlegroups.com?utm_medium\x3demail\x26utm_source\x3dfooter';return true;" onclick="this.href='https://groups.google.com/d/msgid/cp2k/0a1b04bc-ad4c-4cd0-babc-7f694e836288o%40googlegroups.com?utm_medium\x3demail\x26utm_source\x3dfooter';return true;">https://groups.google.com/d/<wbr>msgid/cp2k/0a1b04bc-ad4c-4cd0-<wbr>babc-7f694e836288o%<wbr>40googlegroups.com</a>.<br> </blockquote></div> </blockquote></div></div>