<html><head></head><body><div style="color:#000; background-color:#fff; font-family:Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px"><div dir="ltr" id="yui_3_16_0_ym19_1_1511181693692_130543"><span>Dear Dr. Sham,</span></div><div id="yui_3_16_0_ym19_1_1511181693692_130714" dir="ltr"><br><span></span></div><div id="yui_3_16_0_ym19_1_1511181693692_130584" dir="ltr"><span id="yui_3_16_0_ym19_1_1511181693692_130585">Our purpose is to have fix optimized positions of H2CS (coordinates of constituent atoms) and to put various positions He atom. Your suggestion may not help us. </span></div><div id="yui_3_16_0_ym19_1_1511181693692_130549"> </div><div id="yui_3_16_0_ym19_1_1511181693692_130552" class="signature"><div id="yui_3_16_0_ym19_1_1511181693692_130551"><div id="yui_3_16_0_ym19_1_1511181693692_130550"><font color="#000000" face="comic sans ms" size="3"><br><span style="font-weight:bold;">With regards,</span></font></div><div id="yui_3_16_0_ym19_1_1511181693692_130755"><span style="font-weight:bold;"> </span></div><div id="yui_3_16_0_ym19_1_1511181693692_130756"><font style="font-weight:bold;" face="comic sans ms" size="3">Prof. Suresh Chandra,<br><br>Deputy Director & Professor,<br>Amity Centre for Astronomy & Astrophysics,<br>Amity Institute of Applied Sciences,<br>Amity University, Sector-125, <br>NOIDA 201313, U.P., India<br><br>Email: schandra2@amity.edu;<br> suresh492000@yhoo.co.in<br><br>Mob. +91-9818005663, 8368908608<br></font></div>=========================================</div><span style="background-color:rgb(255, 255, 255);font-weight:bold;">Alexander von Humboldt Fellow (Germany),<br>Former Director, School of Physical Sciences,<br>S.R.T.M. University, Nanded (Maharashtra)</span></div> <div class="qtdSeparateBR"><br><br></div><div style="display: block;" class="yahoo_quoted"> <div style="font-family: Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, Sans-Serif; font-size: 16px;"> <div dir="ltr"><font face="Arial" size="2"> On Friday, 17 November 2017 6:00 AM, "molpro-user-request@molpro.net" <molpro-user-request@molpro.net> wrote:<br></font></div> <br><br> <div class="y_msg_container"><div dir="ltr">Send Molpro-user mailing list submissions to<br></div><div dir="ltr"> <a ymailto="mailto:molpro-user@molpro.net" href="mailto:molpro-user@molpro.net">molpro-user@molpro.net</a><br></div><div dir="ltr"><br></div><div dir="ltr">To subscribe or unsubscribe via the World Wide Web, visit<br></div><div dir="ltr"> <a href="http://www.molpro.net/mailman/listinfo/molpro-user" target="_blank">http://www.molpro.net/mailman/listinfo/molpro-user</a><br></div><div dir="ltr">or, via email, send a message with subject or body 'help' to<br></div><div dir="ltr"> <a ymailto="mailto:molpro-user-request@molpro.net" href="mailto:molpro-user-request@molpro.net">molpro-user-request@molpro.net</a><br></div><div dir="ltr"><br></div><div dir="ltr">You can reach the person managing the list at<br></div><div dir="ltr"> <a ymailto="mailto:molpro-user-owner@molpro.net" href="mailto:molpro-user-owner@molpro.net">molpro-user-owner@molpro.net</a><br></div><div dir="ltr"><br></div><div dir="ltr">When replying, please edit your Subject line so it is more specific<br></div><div dir="ltr">than "Re: Contents of Molpro-user digest..."<br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr">Today's Topics:<br></div><div dir="ltr"><br></div><div dir="ltr"> 1. Re: To understand the reason for difference betweeen two<br></div><div dir="ltr"> outputs for the same situation developed by MOLPRO (Sham K)<br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr">----------------------------------------------------------------------<br></div><div dir="ltr"><br></div><div dir="ltr">Message: 1<br></div><div dir="ltr">Date: Thu, 16 Nov 2017 13:35:06 +0530<br></div><div dir="ltr">From: Sham K <<a ymailto="mailto:shaawm@gmail.com" href="mailto:shaawm@gmail.com">shaawm@gmail.com</a>><br></div><div dir="ltr">To: Molpro-user <<a ymailto="mailto:molpro-user@molpro.net" href="mailto:molpro-user@molpro.net">molpro-user@molpro.net</a>><br></div><div dir="ltr">Subject: Re: [molpro-user] To understand the reason for difference<br></div><div dir="ltr"> betweeen two outputs for the same situation developed by MOLPRO<br></div><div dir="ltr">Message-ID:<br></div><div dir="ltr"> <CAMu9eM+fdgN7xUfdch0nnwN7CuRxGA2+<a ymailto="mailto:kpiJO8K3DfJJMeG7Jw@mail.gmail.com" href="mailto:kpiJO8K3DfJJMeG7Jw@mail.gmail.com">kpiJO8K3DfJJMeG7Jw@mail.gmail.com</a>><br></div><div dir="ltr">Content-Type: text/plain; charset="utf-8"<br></div><div dir="ltr"><br></div><div dir="ltr">Hello Users,<br></div><div dir="ltr"><br></div><div dir="ltr">One simple possibility is to check nuclear repulsion energy to satisfy if<br></div><div dir="ltr">two geometries are the same.<br></div><div dir="ltr"><br></div><div dir="ltr">There is another nice way to check if two structures (with same atoms and<br></div><div dir="ltr">the order in which they are listed is same) with different xyz data are<br></div><div dir="ltr">same. This comes from an elegant algorithm known as Kabsch algorithm - for<br></div><div dir="ltr">details of how it works see - <a href="https://en.wikipedia.org/wiki/Kabsch_algorithm" target="_blank">https://en.wikipedia.org/wiki/Kabsch_algorithm</a><br></div><div dir="ltr"><br></div><div dir="ltr">It calculates an RMSD between two structures. For the case here, using the<br></div><div dir="ltr">calculate_rmsd program from github, download it from<br></div><div dir="ltr"><a href="https://raw.githubusercontent.com/charnley/rmsd/master/rmsd/calculate_rmsd.py" target="_blank">https://raw.githubusercontent.com/charnley/rmsd/master/rmsd/calculate_rmsd.py</a><br></div><div dir="ltr"><br></div><div dir="ltr"><a ymailto="mailto:sham@shree" href="mailto:sham@shree">sham@shree</a>:~/junk$ ./calculate_rmsd.py a.xyz b.xyz<br></div><div dir="ltr">Normal RMSD: 0.305543115084<br></div><div dir="ltr">Kabsch RMSD: 7.14474667163e-06<br></div><div dir="ltr">Quater RMSD: 7.14474667163e-06<br></div><div dir="ltr"><br></div><div dir="ltr">Showing that two structures are indeed the same.<br></div><div dir="ltr"><br></div><div dir="ltr">-Sham<br></div><div dir="ltr">-------------- next part --------------<br></div><div dir="ltr">An HTML attachment was scrubbed...<br></div><div dir="ltr">URL: <<a href="http://www.molpro.net/pipermail/molpro-user/attachments/20171116/07e4af8e/attachment-0001.html" target="_blank">http://www.molpro.net/pipermail/molpro-user/attachments/20171116/07e4af8e/attachment-0001.html</a>><br></div><div dir="ltr"><br></div><div dir="ltr">------------------------------<br></div><div dir="ltr"><br></div><div dir="ltr">Subject: Digest Footer<br></div><div dir="ltr"><br></div><div dir="ltr">_______________________________________________<br></div><div dir="ltr">Molpro-user mailing list<br></div><div dir="ltr"><a ymailto="mailto:Molpro-user@molpro.net" href="mailto:Molpro-user@molpro.net">Molpro-user@molpro.net</a><br></div><div dir="ltr"><a href="http://www.molpro.net/mailman/listinfo/molpro-user" target="_blank">http://www.molpro.net/mailman/listinfo/molpro-user</a><br></div><div dir="ltr"><br></div><div dir="ltr">------------------------------<br></div><div dir="ltr"><br></div><div dir="ltr">End of Molpro-user Digest, Vol 112, Issue 13<br></div><div dir="ltr">********************************************<br></div><br><br></div> </div> </div> </div></div></body></html>