MolStat

Gaussian Input/Output File Viewer
MD Simulation Visualizer/Animator

16, Jan, 2003
Japanese

Introduction

MolStat is a software for molecular visualization. MolStat can read Gaussian input and output files, MOPAC input files, TINKER XYZ files, and infrared/raman spectra(J-CAMP DX file). MolStat can show vibrational animation for each normal modes, and is also possible to write out animation as movie file.

This software is provided to you "AS-IS" and without warranty of any kind. You can try this software freely for purpose of personal or academic use. This software is still underdeveloped, and there are still unstabile functions.


Snapshot

Environment

 probably Windows95R2/98/Me/NT/2000/XP with fast graphic accerelator


Download


Install

  1. Extract downloaded archive file.
  2. Executet MolStat.exe in the archive.

Usage

Load molecule files from "File" - "Open Molecule"

If molecule is written in cartesian coordinate, the file does not include bonding information, so that click "AutoBondConnection" button to construct bonds.


MolStat Animation File (*.mst)

MolStat can visualize animation from MD simulation, etc. For this purpose, there is special file format.

Example

; ";" is symbol of comments
%ATOMCOLOR    8  #FF0000 54.9 ; atom number, color, radius
%ATOMRADIUS   8  54.9 ; atom number, radius
%FILE   1  GAUSSIAN_OUTPUT "Acetone.out"  0 1 0 0 0 1 1 0 0 ; file number, filetype, filename, rotation matrix
%MOL    2  3   010101010  ; molecule number, number of atoms, connection
%COLOR    123 #FF6666  120 ; atom number, color, raeius
%COLOR    12  #66FF66  120
%COLOR    14  #6666FF  120
%MODELTYPE 2 BALL&STICK 0.2 0.1 ; molecule number, modeltype, ball, stick
%TIMESTEP  5.0 ; timestep(fs)
%DATA
%TIME  5.0 ; time (fs)
%FREQ 1 18 1725.15 0.1 ; identifier, mode number, frequency, magnitude
10 1   0.00   0.00   0.00  0.772  0.106  0.627 -0.628  0.286  0.724 -0.102 -0.952  0.287 FREQ 1 ; moltype, file number, posx, posy, posz, 9 rotation matrix elements, frequency identifier 
0 2  14   2.17  -3.63   2.01  12   2.90  -2.94   2.62 123   3.80  -2.09   3.39 ; moltype, molecle number, atom number, x, y, z, (...)
0 2  14   2.28  -3.98  -3.98  12   2.68  -3.32  -3.10 123   3.19  -2.50  -2.00
0 2  14   5.25   0.83   0.82  12   5.78   0.08   0.09 123   6.45  -0.85  -0.82
0 2  14   2.39   1.74   1.90  12   3.01   2.56   2.45 123   3.78   3.59   3.14
0 2  14   2.00   2.17  -3.80  12   2.74   2.53  -2.97 123   3.65   2.97  -1.92
0 2  14  -6.37   0.62   0.60  12  -5.55   0.05  -0.01 123  -4.53  -0.66  -0.77
0 2  14  -3.69  -3.75   2.34  12  -2.94  -3.09   2.94 123  -2.00  -2.26   3.69
0 2  14  -0.71   0.85   6.15  12   0.00   0.18   5.51 123   0.89  -0.65   4.70
0 2  14  -0.86   0.62  -4.84  12  -0.07  -0.05  -5.38 123   0.92  -0.88  -6.06
0 2  14  -3.44  -3.61  -3.78  12  -2.63  -3.08  -3.12 123  -1.62  -2.42  -2.31
0 2  14  -3.73   2.09   2.27  12  -2.84   2.77   2.61 123  -1.72   3.61   3.04
0 2  14  -3.58   2.12  -3.98  12  -2.70   2.56  -3.34 123  -1.60   3.10  -2.54
0 2  14  -0.82   6.35   0.56  12  -0.02   5.87  -0.14 123   0.99   5.27  -1.01
0 2  14  -0.70  -5.08   0.98  12   0.12  -5.67   0.40 123   1.15  -6.41  -0.33

%TIME  10.0
%FREQ 1 18 1724.49 0.1
10 1   0.00   0.00   0.00  0.767  0.118  0.631 -0.631  0.316  0.709 -0.116 -0.942  0.316 FREQ 1 
0 2  14   2.18  -3.65   2.03  12   2.92  -2.96   2.62 123   3.84  -2.11   3.36
0 2  14   2.28  -4.01  -4.01  12   2.67  -3.36  -3.11 123   3.14  -2.55  -2.00
0 2  14   5.25   0.83   0.81  12   5.79   0.08   0.09 123   6.46  -0.86  -0.81
0 2  14   2.41   1.71   1.90  12   3.03   2.55   2.43 123   3.81   3.59   3.09
0 2  14   2.00   2.19  -3.82  12   2.74   2.50  -2.97 123   3.67   2.89  -1.92
0 2  14  -6.38   0.60   0.59  12  -5.54   0.05  -0.01 123  -4.50  -0.64  -0.76
0 2  14  -3.72  -3.77   2.37  12  -2.95  -3.12   2.97 123  -2.00  -2.30   3.71
0 2  14  -0.73   0.86   6.13  12   0.01   0.20   5.50 123   0.92  -0.62   4.72
0 2  14  -0.88   0.60  -4.85  12  -0.06  -0.06  -5.36 123   0.97  -0.88  -6.00
0 2  14  -3.45  -3.61  -3.78  12  -2.61  -3.10  -3.14 123  -1.56  -2.47  -2.34
0 2  14  -3.75   2.10   2.31  12  -2.84   2.77   2.61 123  -1.70   3.61   2.99
0 2  14  -3.59   2.14  -4.01  12  -2.69   2.54  -3.38 123  -1.56   3.04  -2.61
0 2  14  -0.84   6.34   0.54  12  -0.02   5.89  -0.16 123   1.01   5.33  -1.03
0 2  14  -0.71  -5.10   1.01  12   0.14  -5.68   0.44 123   1.19  -6.41  -0.27
      

History

6 Oct. 2002 -- MolStat Developing Preview Version 0.901
19 Nov. 2002 -- MolStat Developing Preview Version 0.902
25 Nov. 2002 -- MolStat Developing Preview Version 0.903
26 Nov. 2002 -- MolStat Developing Preview Version 0.904
3 Dec. 2002 -- MolStat Developing Preview Version 0.905
4 Dec. 2002 -- MolStat Developing Preview Version 0.906
5 Dec. 2002 -- MolStat Developing Preview Version 0.907
12 Dec. 2002 -- MolStat Developing Preview Version 0.908
15 Jan 2003 -- MolStat English 0.908en0
16 Jan 2003 -- MolStat English 0.908en1

Name: NOMOTO Tomonori
URL: http://T.NOMOTO.org/MolStat/


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NOMOTO Tomonori(PGP Public Key)