<div>Dear Marcella</div>Thanks for your reply. I did apply WALL associated with collective variables (coordination numbers of C and O in parent molecule) for my system. I applied a lower limit (found using an unbiased MD run) of coordination numbers using WALL_MINUS.<div>But the water molecule was still moving away inside the system during metaD. run, probably because the system could still maintain the wall limit with/without water. Could you please suggest any different way to apply WALLS for this system? Also, you suggested using an external potential confining the coordinates within a certain region of space. Could you please explain the keywords of CP2K to apply external potential for any system? </div><div><br></div><div>Regards</div><div>Aditya</div><div><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Wednesday, October 19, 2022 at 2:35:04 PM UTC+5:30 Marcella Iannuzzi 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 Aditya<div><br></div><div>You can use either a WALL associated to some collective variable, or an external potential confining the coordinates within a certain region of space. </div><div>Regards</div><div>Marcella<br><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Tuesday, October 18, 2022 at 2:56:02 PM UTC+2 <a href data-email-masked rel="nofollow">goyal.a...@gmail.com</a> 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 class="gmail_quote"><div dir="auto" class="gmail_attr">On Tuesday, October 11, 2022 at 9:24:13 PM UTC+5:30 <a rel="nofollow">mattwa...@gmail.com</a> 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">Hello,<div>sorry I don't know the metadynamics code well.</div><div>Maybe if you explain very clearly what you want to achieve and include your input / output you can get more assistance.</div><div>Matt<br><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Thursday, 6 October 2022 at 14:41:14 UTC+1 <a rel="nofollow">goyal.a...@gmail.com</a> 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 All,<div><br></div><div>I am performing metadynamics simulation on my system having 2 molecules to perform a reaction with coordination numbers as 2 collective variables. Unfortunately, a molecule is moving far apart from the other molecule (fixed) during simulation. So, I wanted to apply a boundary to restrict the motion of moving molecule within a certain distance (d) from the fixed molecule, to maintain enough interactions to perform this reaction. I've seen some answers suggesting restraining the distance using a collective variable but that would fix the moving molecule to distance 'd ' in space and restrict its motion for distances ≤ d . Ideally, the moving molecule should stay within distance : (0 to d ) for a good metadynamics run. Any suggestions would be appreciated. </div><div><br></div><div>Regards</div><div><br></div><div>Aditya</div></blockquote></div></blockquote></div></blockquote></div></blockquote></div>
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