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Good afternoon, Marcella:</div><div></div><div></div><div><br></div><div>>Your time-step is too large.</div><div><br></div><div>Thank you, dear Marcelle<br></div><div>I will test a shorter step.</div><div></div><div>I think you might got it right,</div><div>because, <br></div><div>the instabilities always concern the dynamics of Hydrogen stretchings only,<br></div><div>but they are at the higher frequency range.</div><div><br></div><div>>
Is there a reason why you use Langevin dynamics rather than a more standard thermostat?
</div><div><br></div><div>In the input <br></div><div>for all the atoms<br></div><div>I instruct <br></div><div></div><div>DO_LANGEVIN F<br></div><div><br></div><div>Therefore, <br></div><div>I thought the simulation should be B-O</div><div>not Langevin.</div><div></div><div>I suspect that <br></div><div>still<br></div><div>the thermostat to accomodate the dynamiocs is <br></div><div>not well defined.</div><div><b>Would you give me a hint? </b><br></div><div><br></div><div>"My" current configuration in the input <br></div><div>is according to several examples I found on-line</div><div> and some intuitive guess-trials.</div><div><br></div><div>The idea is <br></div><div>
with least possible compromise
</div><div>to try to simulate delocalised water dynamics <br></div><div></div><div>to interact with the copper ion which is doublet while it is complexed by aminoacids</div><div></div><div>This would be the simplest but yet the most comprehencive <br></div><div>simulation to approach a vision of what is going on in comparable complexes in vivo.<br></div><div><br></div><div>>Are you sure that diagonalization+smearing <br></div><div>>is the most efficient optimisation scheme for your system?</div><div><br></div><div>I studied the examples and various inputs
on-line.</div><div>Indeed, my setting may not be adequate.<br></div><div>Would you recommend to set it different?</div><div></div><div><br></div><div>During the past 4 days I tuned the ambition a bit down</div><div>and started testing a dry complex in vacuum.</div><div>It runs well without any issues: please see T0.xyz</div><div><br></div><div>Today, I moved one step ahead adding one water</div><div>but</div><div>this time I do instruct <br></div><div>the three atoms of the water <br></div><div>
by Langevin, <br></div><div>while the rest is by BO.</div><div><br></div><div>However, I am not sure that in such case as much quantum dynamics</div><div>of interaction of water with the copper would be respected:</div><div>please see the attached T1a files<br>
</div><div><br></div><div>Carole and me will acknowledge you advise in the manuscript we are working on.</div><div><br></div><div>Thank you.</div><div>Wish you a nice day,</div><div>Victor<br>
</div><div><br></div><div><br></div><div><br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Jul 15, 2021 at 11:29 AM Marcella Iannuzzi <<a href="mailto:marci...@gmail.com">marci...@gmail.com</a>> 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">Hi Victor,<div><br></div><div>Your time-step is too large. </div><div>Is there a reason why you use Langevin dynamics rather than a more standard thermostat?</div><div>Are you sure that diagonalization+smearing is the most efficient optimisation scheme for your system?</div><div><br></div><div>Kind regards</div><div>Marcella<br><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Monday, July 12, 2021 at 3:08:36 PM UTC+2 <a href="mailto:vo...@gmail.com" target="_blank">vo...@gmail.com</a> 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"><br><div>good day</div><div>I wish to ask about the observed structural instability upon BO-MD</div><div>of a hydrated copper-proline complex.</div><div>It starts ok, but later hydrogens start to fly away.</div><div>Thank you.</div><div>Victor<br></div></blockquote></div>
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