<div dir="ltr"><div dir="ltr"><div>Dear Patrick,</div><div>Since I have done AIMD of simple ions in water that is out of 64 water molecules replaced one water molecule and placed H+ ion in it so i am expecting to see grotthus mechanism. I am attaching the input files and trajectory files. Please give it a quick look and reply if I am doing something wrong.</div><div><br></div><div>Yours sincerely</div><div>Akshay Malik<br></div><div><div class="gmail_chip gmail_drive_chip" style="width:396px;height:18px;max-height:18px;background-color:rgb(245,245,245);padding:5px;color:rgb(34,34,34);font-family:arial;font-style:normal;font-weight:bold;font-size:13px;border:1px solid rgb(221,221,221);line-height:1"><a href="https://drive.google.com/file/d/1r2HPG-MvTK6UvZFjgXnM-IkEfZhSIeiy/view?usp=drive_web" target="_blank" style="display:inline-block;max-width:366px;overflow:hidden;text-overflow:ellipsis;white-space:nowrap;text-decoration:none;padding:1px 0;border:none"><img style="vertical-align: bottom; border: none;" src="https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png"> <span dir="ltr" style="color:rgb(17,85,204);text-decoration:none;vertical-align:bottom">WATER-pos-1.xyz</span></a><img src="//ssl.gstatic.com/ui/v1/icons/common/x_8px.png" style="opacity: 0.55; cursor: pointer; float: right; top: -1px; display: none;"></div><div class="gmail_chip gmail_drive_chip" style="width:396px;height:18px;max-height:18px;background-color:rgb(245,245,245);padding:5px;color:rgb(34,34,34);font-family:arial;font-style:normal;font-weight:bold;font-size:13px;border:1px solid rgb(221,221,221);line-height:1"><a href="https://drive.google.com/file/d/1SUH4LUEqy1bAZ0AiOrx0gATttp7K4szy/view?usp=drive_web" target="_blank" style="display:inline-block;max-width:366px;overflow:hidden;text-overflow:ellipsis;white-space:nowrap;text-decoration:none;padding:1px 0;border:none"><img style="vertical-align: bottom; border: none;" src="https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png"> <span dir="ltr" style="color:rgb(17,85,204);text-decoration:none;vertical-align:bottom">water.inp</span></a><img src="//ssl.gstatic.com/ui/v1/icons/common/x_8px.png" style="opacity: 0.55; cursor: pointer; float: right; top: -1px; display: none;"></div><div class="gmail_chip gmail_drive_chip" style="width:396px;height:18px;max-height:18px;background-color:rgb(245,245,245);padding:5px;color:rgb(34,34,34);font-family:arial;font-style:normal;font-weight:bold;font-size:13px;border:1px solid rgb(221,221,221);line-height:1"><a href="https://drive.google.com/file/d/1mKGUwOqDbGH49Un4ciK2Kc1nPTdMRMxe/view?usp=drive_web" target="_blank" style="display:inline-block;max-width:366px;overflow:hidden;text-overflow:ellipsis;white-space:nowrap;text-decoration:none;padding:1px 0;border:none"><img style="vertical-align: bottom; border: none;" src="https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png"> <span dir="ltr" style="color:rgb(17,85,204);text-decoration:none;vertical-align:bottom">wateralter.xyz</span></a><img src="//ssl.gstatic.com/ui/v1/icons/common/x_8px.png" style="opacity: 0.55; cursor: pointer; float: right; top: -1px; display: none;"></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Feb 11, 2019 at 6:34 PM Patrick Gono <<a href="mailto:patric...@gmail.com">patric...@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"><div dir="ltr"><div>Dear Akshay,</div><div><br></div><div>A visualization software is just that -- a tool that allows you to visually inspect the simulated trajectory. If no proton transfer happened, there is nothing to visualize. Assuming that there is some proton transfer happening, the CPK representation should be actually the best. Here, the bonds are displayed between close-by atoms in the initial configuration, and then remain during the simulation. Hence, if a proton did move from one water molecule to another, you should see ridiculously stretched O-H bonds in your MD. The Dynamic Bonds representation only uses a very simple cutoff distance bellow which a bond is displayed. So, naturally, there will be some bond breaking and formation of new bonds during the course of the simulation, but it may be hard to spot this using this representation. Plus, if you use a large cutoff, hydrogen bonds to neighboring water molecules might be shown as real bonds occasionally, which is not what you probably are looking for.<br></div><div><br></div><div>If you have dozens and dozens of picoseconds worth of trajectory to comb through, and you do not trust the CPK representation for some reason, you can also write a short script to analyze the trajectory yourself. For example, you could calculate the two shortest bonds for each oxygen atom in the first snapshot, and then track the length of these bonds over time. At some point, if a proton transfer occurs, the length of one of these bonds will exceed a given threshold (say, around 1.3 A). You then simply output the snapshot index and go look it up in VMD to see what is happening. But this is basically what the CPK representation already visualizes.</div><div><br></div><div>Are you sure that proton transfer can be observed in your simulation? Are you simulating pure water, or do you also include an extra proton (or H3O+)? What parameters did you use for the simulation? How long is your trajectory in physical terms -- do you expect to observe proton transfer on this timescale? Could you share your CP2K input, initial water structure file, and possibly (if size allows) the simulated trajectory, please? You can upload the trajectory to dropbox or google drive and send me the link if it is too large.<br></div><div><br></div><div>Yours sincerely,</div><div>Patrick Gono<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, 8 Feb 2019 at 13:46, Akshay Malik <<a href="mailto:akshayma...@gmail.com" target="_blank">akshayma...@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"><div dir="ltr"><div dir="ltr">Dear Patrick,</div><div dir="ltr"><br></div><div>I have used VMD to analyze the trajectory file but I am not able to see the quantum effects such as proton transfer in CPK Representation but in DynamicBonds representation there is some sort of bond making and breaking. Can I consider DynamicBonds representation as quantum effects? <br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Feb 8, 2019 at 4:37 PM Patrick Gono <<a href="mailto:patric...@gmail.com" target="_blank">patric...@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"><div dir="ltr"><div dir="ltr"><div>Dear Akshay,</div><div><br></div><div>I suggest VMD, which can be found at <a href="https://www.ks.uiuc.edu/Research/vmd/" target="_blank">https://www.ks.uiuc.edu/Research/vmd/</a></div><div><br></div><div>Yours sincerely</div><div>Patrick Gono<br></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, 8 Feb 2019 at 05:35, Akshay Malik <<a href="mailto:akshayma...@gmail.com" target="_blank">akshayma...@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"><div dir="ltr">I have done AIMD of liquid water by using cp2k. I want to see the bond breaking and proton transfer by grotthuss mechanism. Please suggest some visualisation softwares. <br></div>
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