<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><span style="background-color: rgb(255, 255, 255);" class="">Dear Abir Shadman,</span><br style="background-color: rgb(255, 255, 255);" class=""><span style="background-color: rgb(255, 255, 255);" class=""><br class=""></span><div class=""><span style="background-color: rgb(255, 255, 255);" class="">For the first question, my understanding (but others are more knowledgeable than me) you can use tot_charge to specify that the total charge of your system is the one of your phosphate molecule (say -2), but whether this charge goes all on the phosphate depends on the relative affinities of the different components of your system. Tot_charge only controls the total amount of electrons in your simulation, it does not enforce by itself where these electrons will go. For the same reason it cannot be used to model a sheet of charge placed above the NR. </span><br style="background-color: rgb(255, 255, 255);" class=""><br style="background-color: rgb(255, 255, 255);" class=""><span style="background-color: rgb(255, 255, 255);" class="">On the other hand, for this purpose one possible way (there might be others) would be to use the Environ module for QE (</span><a class="moz-txt-link-abbreviated" href="http://www.quantum-environ.org" style="background-color: rgb(255, 255, 255);">www.quantum-environ.org</a><span style="background-color: rgb(255, 255, 255);" class="">). The new release of the module (which will come out later today or tomorrow) allows you to consider arbitrary fixed distributions of charges inside the simulation cell, thus also sheets of charges (but also wires or point-like charges). Whether this simulation converges, makes sense, is physical depends a lot on your system and set ups, but you can try playing with it. If you want to use the module and need help with the set up of the calculation, feel free to contact me. </span></div><div class=""><br style="background-color: rgb(255, 255, 255);" class=""><span style="background-color: rgb(255, 255, 255);" class="">Best regards,</span><br style="background-color: rgb(255, 255, 255);" class=""><br style="background-color: rgb(255, 255, 255);" class=""><span style="background-color: rgb(255, 255, 255);" class="">Oliviero Andreussi</span><br style="background-color: rgb(255, 255, 255);" class=""><div><br class=""><blockquote type="cite" class=""><div class="">On 12 Jan 2016, at 22:52, Abir Shadman <<a href="mailto:abirshadman@gmail.com" class="">abirshadman@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div dir="ltr" class=""><div class="gmail_default"><font face="arial, helvetica, sans-serif" class="">Thanks Dr. </font>Paulatto for your reply. However about my first question, I am trying to relax a charged phosphate molecule (say doubly charged) over a MoS2 Nanoribbon. They are attracted together by van der waals force as reported in many papers. My question was how to do the bfgs relaxation considering the charged molecule? I can simulate a, say neutral phosphoric acid over the NR, but what I have to do incorporate the charge?</div><div class="gmail_default"><br class=""></div><div class="gmail_default">And about your reply to my second question, will tot_charge keyword consider a sheet charge over neutral NR? </div><div class="gmail_default"><br class=""></div><div class="gmail_default">Thanks again. I look forward to hearing from you. It will be very helpful from me to get responses from other QE users also.</div><div class="gmail_default"><br class=""></div><div class="gmail_default">Best,</div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Tue, Jan 12, 2016 at 4:40 AM, Abir Shadman <span dir="ltr" class=""><<a href="mailto:abirshadman@gmail.com" target="_blank" class="">abirshadman@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr" class=""><div style="font-family:arial,helvetica,sans-serif" class="">Dear researchers,</div><div style="font-family:arial,helvetica,sans-serif" class=""><br class=""></div><div style="font-family:arial,helvetica,sans-serif" class="">I have 2 questions:</div><div style="font-family:arial,helvetica,sans-serif" class=""><br class=""></div><div style="font-family:arial,helvetica,sans-serif" class="">1. I am trying to relax a charged phosphate molecule over a MoS2 Nanoribbon and then do scf and bands calculation. I am informed of the such simulations for neutral multilayered TMDCs. That's why, I basically need to know how to incorporate these negative charges in simulation?</div><div style="font-family:arial,helvetica,sans-serif" class=""><br class=""></div><div style="font-family:arial,helvetica,sans-serif" class="">2. If I want to do bfgs,scf and bands simulation of a MoS2 NR with a sheet charge over it, will it be possible? How to consider sheet charge in QE?</div><div style="font-family:arial,helvetica,sans-serif" class=""><br class=""></div><div style="font-family:arial,helvetica,sans-serif" class="">I am relatively new to QE. I have done some basic simulations in QE. If these types of questions with charged molecules are already answered, can anyone atleast provide me those links/sources? </div><div style="font-family:arial,helvetica,sans-serif" class=""><br class=""></div><div style="font-family:arial,helvetica,sans-serif" class="">Thanks in advance.</div><div class=""><br class=""></div><div style="font-family:arial,helvetica,sans-serif;display:inline" class="">Best,</div><br class=""><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class=""><font face="verdana, sans-serif" class="">Abir Shadman</font></div><font face="verdana, sans-serif" class="">Dept. of EEE,<span style="font-size:12.8px" class="">BUET.</span></font></div><div class=""><br class=""></div></div></div></div></div></div></div></div>
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</blockquote></div><br class=""><br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div class="gmail_signature"><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class=""><font face="verdana, sans-serif" class="">Abir Shadman</font></div><font face="verdana, sans-serif" class="">Dept. of EEE,<span style="font-size:12.8px" class="">BUET.</span></font></div><div class=""><br class=""></div></div></div></div></div></div></div></div>
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