[molpro-user] Molpro-user Digest, Vol 112, Issue 13

[Prof. Suresh Chandra]

Dear Dr. Sham,
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.  
With regards, Prof. Suresh Chandra,

Deputy Director & Professor,
Amity Centre for Astronomy & Astrophysics,
Amity Institute of Applied Sciences,
Amity University, Sector-125, 
NOIDA 201313, U.P., India

Email: schandra2 at amity.edu;
       suresh492000 at yhoo.co.in

Mob. +91-9818005663, 8368908608
=========================================Alexander von Humboldt Fellow (Germany),
Former Director, School of Physical Sciences,
S.R.T.M. University, Nanded (Maharashtra) 

    On Friday, 17 November 2017 6:00 AM, "molpro-user-request at molpro.net" <molpro-user-request at molpro.net> wrote:
 

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Today's Topics:

  1. Re: To understand the reason for difference betweeen two
      outputs for the same situation developed by MOLPRO (Sham K)


----------------------------------------------------------------------

Message: 1
Date: Thu, 16 Nov 2017 13:35:06 +0530
From: Sham K <shaawm at gmail.com>
To: Molpro-user <molpro-user at molpro.net>
Subject: Re: [molpro-user] To understand the reason for difference
    betweeen two outputs for the same situation developed by MOLPRO
Message-ID:
    <CAMu9eM+fdgN7xUfdch0nnwN7CuRxGA2+kpiJO8K3DfJJMeG7Jw at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hello Users,

One simple possibility is to check nuclear repulsion energy to satisfy if
two geometries are the same.

There is another nice way to check if two structures (with same atoms and
the order in which they are listed is same) with different xyz data are
same. This comes from an elegant algorithm known as Kabsch algorithm - for
details of how it works see - https://en.wikipedia.org/wiki/Kabsch_algorithm

It calculates an RMSD between two structures. For the case here, using the
calculate_rmsd program from github, download it from
https://raw.githubusercontent.com/charnley/rmsd/master/rmsd/calculate_rmsd.py

sham at shree:~/junk$ ./calculate_rmsd.py a.xyz b.xyz
Normal RMSD: 0.305543115084
Kabsch RMSD: 7.14474667163e-06
Quater RMSD: 7.14474667163e-06

Showing that two structures are indeed the same.

-Sham
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