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Winmostar

for Windows/98/Me/NT/2000/XP

Copyright (C) 2001 Norio Senda All Rights Reserved

Japanese

Table of contents　　
1, in beginning
2, installation/un installation
3, usage
4, FAQ
5, about copyright reprinting and the like
6, past record

1, in beginning
　As for Winmostar, it is the software which from the modeling of the molecule actualizes to the indication of the molecular tracked calculation and calculation result on Windows.
　The maximum number of atoms: Concerning the modeling of the molecule, perhaps 99,999 atoms (to 100,000 atoms verification end).


It returns

2, installation/un installation
2-1 installation
　It downloaded When the exe file is executed, it is thawed. c:\ winmos3 becomes the folder of default.
　[Start] in menu and desktop Winmostar Is added automatically.

　V2.After of the 0 became Delphi edition, entry to registry stopped doing. Because the execution time as in VB edition is unnecessary, copying the folder which is installed in other PC, it reaches the point where it can execute. As for executable file winmostar.It is exe.
　It does not install to HDD and also the [te], it is possible to execute from MO and USB memory.

　It does not prohibit the redistribution for the workshop at the university and the like, but the fact that it cannot grasp the number of users is trouble. When the workshop is executed, if it is possible, when you communicate with the mail, it is saved. To continue distribution as a free software, voice of the user most becomes encouragement.

2-2 version upgrade
　It can upgrade with the same method as installation. Because when Winmostar is started, it becomes error, please note.

2-3 un installation
　Un it can install with just the deletion of the folder and the shortcut which are installed.

With 2-4 LinuxInstallationWith execution
The version of Wine which is installed is inspected.
# rpm - qa | grep wine
wine-200xxxxx-x
wine-devel-200xxxxx-x
If version is old, un it installs.
# rpm - e wine-devel
# rpm - e wine
http://www.winehq.wine which is downloaded from com/is installed.
# rpm - ivh wine-200xxxxx-xxxxxx-xxxx.rpm
Execution
# wine winmostar


It returns

3, usage
3-1 summary
　Winmostar has designated Z-Matrix (internal coordinates) as the base, but there is no knowledge of Z-Matrix, in order for the modeling of the molecule to be possible, it is designed. The result where it moved & turned is converted the atom and the atomic group to Z-Matrix automatically on the picture. The case of conversion, in order for original connection relationship not to change, it is considered. If there is the knowledge of Z-Matrix, also it is possible to operate Z-matrix directly.

　Not only Z-Matrix coordinate of the MOPAC type which was drawn up with other method, it is possible also XYZ to read coordinate such as PDB type ([kateshian] coordinate). When XYZ coordinate is read, it is converted to Z-Matrix automatically. It is possible also to retain the coordinate of the molecule which it drew up with various types.

　As for molecular tracked indication, the GPT file which was drawn up making use of GRAPH keyword is used.
　ChemscapeChimeWithMOLEKELIt supports also starting.

3-2 setting file
　atoms1.wmx the maximum is number of atoms and the setting file of color of the atom. Default of the maximum number of atoms has become 20,000 atom. When the number of atoms above this is handled, atoms1.The first line of wmx is corrected. When it enlarges too much, because there are times when the program stops standing up, please note.
　V3.After of the 09 reached the point where the maximum number of atoms is expanded automatically, but in the point of stability and the like, we recommend the one which is set with the setting file.

3-3 How to use the mouse
Keyboard The left button The left button + drug The right button The right button + drug
It is not Selection Revolution Selection + part substitution Enlargement reduction
Shift 　 　 Selection + atomic deletion 　

3-4 Explanation of menu
[File]
[New] The picture is initialized.
[You open] The molecule is read from the file.
[Import] Structure and quality value are input from the calculation result file. It is the same as those which is the calculation menu.
[Superscription retention] The molecule of compilation centralization is retained.
[Acquiring name, retention] Inputting new name into the file name box, it retains.
[Superposition of molecule] The molecule is superposed.
　/[Addition] Adding the molecule which you pile up, you pile up and move to indicatory mode. You pile up with the plane surface which is decided in 3 points which are appointed in advance. The 1st point is put in starting point, the 2nd point is put on X axis, the 3rd point is put on XY plane surface.
During pile indicating it cannot compile the molecule. You pile up with Z-shift and shift the surface, you pile up by the fact that the blue circle it indicates and with Circle can verify the molecule. [Del] The molecule which is indicated with the blue circle is deleted.
When it ends pile indicatory mode, it returns to usual monad indicatory mode. When reading the molecule from the file, it returns to monad indicatory mode. When adding the molecule which you pile up, it adds from monad indicatory mode.
　/[You pile up, indication] You pile up from monad indicatory mode and change to indicatory mode.
　/[Monad indication] From pile indicatory mode it changes to monad indicatory mode.
[Editor starting] The original file of the indicatory molecule is opened with the editor.
[With XYZ type retention] When retaining the MOPAC type it retains with XYZ type.
[Default profile
　Reading (P)]
[GEMS type]
[End] It ends Winmostar.


[Compilation]
As for compilation of the molecule, in many cases, the operation of doing vis-a-vis the selective atom (with red circle in thick line indication) and the front selective atom (with red circle in thin line indication) becomes the basis. The selective atom can click the atom on the molecular screen, or can modify by the fact that line on the Z-Matrix screen is clicked. The front selective atom is the reference atom of one ago.
For example atomic deletion selects the atom which we would like to delete first, compilation of the pull-down menu (E)/with atomic deletion (or [Del] button) does.
As for part movement revolution deletion, (excluding the front selective atom, the atomic group which has been connected to the selective atom,) collecting it operates.
As for the connection indication with Winmostar, distance between atoms harmony *1 of covalent bond radius.Connection is indicated in when it is smaller than 15 (default value). There is no distinction such as double bond. When we would like to modify connection in order to do part movement revolution deletion, [connection addition] with [it can modify connection deletion].
Operation such as atomic addition, atomic movement and part revolution is cancelled midway, you remove the check of the pull-down menu, or push the Esc key.
[Part substitution] is possible even with method under, but it is substituted with the part of part [uinto] ゙ [u] by also the fact that the right it clicks the atom.
[Atomic deletion] even with Shift key + mouse right click becomes similar operation.
[You reset to origin] You reset on the basis of the compilation operation of the molecule. You can reset only 1 times.
[Direct compilation] The coordinate data is compiled directly with the editor.
[Rotary method]
[Free rotation]
　/[X axial revolution]
　/[Y axial revolution]
　/[Z axial revolution)]
[Atomic addition] The atom is added. [Add] It is the same as the button.
[Atomic movement] The atom which is selected by the drug doing the mouse is moved.
[Atomic deletion] The atom which it selects is deleted. [Del] It is the same as the button.
[Element modification] Element name of the atom which it selects is modified. [Chng] It is the same as the button.
[Hydrogen addition] Hydrogen is added.
　/[All atom] Hydrogen is added to all atom automatically.
　/[1 atoms] Hydrogen is added to the selective atom automatically.
　/[1 atoms (H1)] Hydrogen 1 is added to the selective atom.
　/[1 atoms (H2)] Hydrogen 2 is added to the selective atom.
　/[1 atoms (H3)] Hydrogen 3 is added to the selective atom.
[Hydrogen deletion] Hydrogen is deleted.
[Part substitution] The atom which it selects is substituted with the part of part [konbobotsukusu]. - CHCH- "" "" "" - CH- "" with the part in order to make polycyclic structure, becomes the structure to which the carbon atom gets near on front selective atomic side. [Rep] It is the same as the button.
[Part revolution] Around the axis which passes by the front selective atom and the selective atom, the atomic group of selective atomic side it turns. When two selective atoms ago, furthermore two atoms are selected, dihedral angles around the axis of rotation are indicated.
[Bond angle modification] Focusing on the front selective atom bond angle is modified. Because the atomic group of selective atomic side turns with plane surface on the picture, when after turning, it does the molecule, various deformation is possible.
[Part movement] The atomic group of selective side is moved.
[Part deletion] The atomic group of selective side is deleted.
[Part free rotation] The atomic group of selective side it turns freely.
[Connection addition] Connection is added between the front selective atom and the selective atom.
[Connection deletion] Connection is deleted.
[Number exchange] Number of the selective atom and the front selective atom is exchanged.
[Line changing of atom]
[Connection regeneration] After connecting all atom regeneration, it redraws.
[Part register] It registers the molecule of compilation centralization as the part. It is necessary to select the terminal atom which it makes connect.
[Part deletion] The register of the part is deleted.
[Movement] The molecule is moved to up and down left and right.
[Starting point return] Starting point is reset to the center of the picture.
[Center of gravity starting point] When there is check, always center of gravity is adjusted starting point.
[Starting point setting] The atom which it selects is set to starting point. When in [center of gravity starting point] being check, it does not operate.
[Early orientation] You reset to the orientation at the time of the molecular reading 込.
[Z-Matrix]
　/[Atomic addition (E)] The atom of element [uinto] ゙ [u] is added. After clicking we would like to put in place the atom, 3 atoms which show connection relationship are clicked.
　/[Dummy atomic addition] The dummy atom is added.
　/[2 interfacial angle modifications] 2 interfacial angles of Z-Matrix are modified.
　/[Modification of connection relationship] The connection relationship of Z-Matrix is modified.
　/[Atomic movement (Z-Mat)] By the fact that 1 atoms are moved, it moves also the atom which to the connection relationship of Z-Matrix is.
　/[Z-Matrix regeneration] Z-Matrix regeneration is done. Also connection relationship is done regeneration.
[In addition]
　/[Connection-related retention] When check has entered, at the time of molecular compilation connection relationship that tries does not change.
　/[XYZ coordinate retention] When check has entered, changing connection relationship, in order for XYZ coordinate position not to change, connection long bond angle and the like is corrected automatically.
　/[Coordinate reversal] It converts to the enantiomer.
　/[Enantiomer formation] The enantiomer is formed.
　/[In clipboard
　　　Sticking]		 The molecular screen is stuck to the clipboard.

[Indication]
[All indication] The molecular screen is expanded to the whole window.
[Slider indication] The zoom slider is indicated.
[Standard color] Color scheme, is selected from Winmostar, GaussView and old Winmostar mode.
[Color modification] Atomic color, background color, connection color and letter color are modified.
[Number indication] Number and element name are indicated.
[All the atomic indications] It indicates also the dummy atom and the like.
[Selective atomic marker] The selective atom is indicated with the mark of the red circle.
[Molecular information display] The information regarding the molecule is indicated in inside the window.
[Mesh indication] The grid is indicated.
[Ball&Stick] Type of Ball&Stick indication is selected.
[Zoom] Enlargement it reduces indicates.
[Spatial filling up model] The spatial filling up model is indicated.
[Far method] Using far method, it indicates.
[3D] 3D it indicates.
[VRML] It indicates with VRML, (necessary for VRML [biyuwa] to be installed it is,).
[SIM VRML View] The download page of VRML [biyuwa] of the SIM corporation is indicated.
[Cosmo Player] The download page of Cosmo Player is indicated.
[Facio] Facio is started.
[Facio Path] The pass of Facio is appointed.
[Facio Homepage] The download page of Facio is indicated.
[Mercury] Mercury is started. When the extension of the file while reading is CIF, the CIF file is read.
[Mercury Path] The pass of Mercury is appointed.
[CCDC (Mercury) HP] Mercuryのダウンロードページを表示します。
［ChemscapeChime］ ChemscapeChimeがインストールされている場合、新しいウィンドウでChemscapeChimeを起動します。
［Chimeマニュアルページ］ ChemscapeChimeのマニュアルページを表示します。
［Chimeダウンロードページ］ ChemscapeChimeのページを表示します。
［光線追跡法(povray)］ PovRayがインストールされている場合、光線追跡法で表示します。
［Povrayのパス］ PovRayのパスを指定します。
［Povrayのパラメータ］ PovRayのパラメータを指定します。
［Povrayのホームページ］ PovRayのダウンロードページを表示します。
［画像固定］ 右上の画像が変わらないようにします。
[Indication]
[All indication] The molecular screen is expanded to the whole window.
[Slider indication] The zoom slider is indicated.
[Standard color] Color scheme, is selected from Winmostar, GaussView and old Winmostar mode.
[Color modification] Atomic color, background color, connection color and letter color are modified.
[Number indication] Number and element name are indicated.
[All the atomic indications] It indicates also the dummy atom and the like.
[Selective atomic marker] The selective atom is indicated with the mark of the red circle.
[Molecular information display] The information regarding the molecule is indicated in inside the window.
[Mesh indication] The grid is indicated.
[Ball&Stick] Type of Ball&Stick indication is selected.
[Zoom] Enlargement it reduces indicates.
[Spatial filling up model] The spatial filling up model is indicated.
[Far method] Using far method, it indicates.
[3D] 3D it indicates.
[VRML] It indicates with VRML, (necessary for VRML [biyuwa] to be installed it is,).
[SIM VRML View] The download page of VRML [biyuwa] of the SIM corporation is indicated.
[Cosmo Player] The download page of Cosmo Player is indicated.
[Facio] Facio is started.
[Facio Path] The pass of Facio is appointed.
[Facio Homepage] The download page of Facio is indicated.
[Mercury] Mercury is started. When the extension of the file while reading is CIF, the CIF file is read.
[Mercury Path] The pass of Mercury is appointed.
[CCDC (Mercury) HP] The download page of Mercury is indicated.
[ChemscapeChime] When ChemscapeChime is installed, ChemscapeChime is started in the new window.
[Chime manual page] The manual page of ChemscapeChime is indicated.
[Chime download page] The page of ChemscapeChime is indicated.
[Ray tracing method (povray)] When PovRay is installed, it indicates with ray tracing method.
[The pass of Povray] The pass of PovRay is appointed.
[The parameter of Povray] The parameter of PovRay is appointed.
[The home page of Povray] The download page of PovRay is indicated.
[Picture fixing] The picture with respect to the right that tries does not change.
[Calculation]
The fact that it is attached to Winmostar is MOPAC6, MOPAC7 and CNDO/S. It downloads the other program, from respective HP and/or the register becomes necessary.
MOPAC93: Presently procurement failure
GAMESS: GAMESSIt corresponds to WinGAMESS and PC-GAMESS.
MOLEKEL:MOLEKEL
MOSF V1: Presently procurement failure
MOLEKEL: MOLEKEL
MOSF V1: Presently procurement failure
[MOPAC6W70 START] The MOPAC6 input file is formed with present molecular keyword, to calculation can point. After calculation the output file is opened with the editor who is appointed automatically at “the place of the editor”.
[MOPAC7W70 START] The MOPAC7 input file is formed, to calculation can point.
[MOPACX (2) start] It is similar to MOPAC6. (When it is not, it becomes invalid)
[Editing out] The standard output file of MOPAC (.out) You open with the designated editor.
[Editing arc] The output summary file of MOPAC (.arc) You open with the designated editor.
[Molecular tracked indication] When outputting graphics in the calculation, (it is output with keyword graph,), reading the output, it indicates the molecular track. Also 3D indication is possible.
[Import]
　/[Arc] Reading the structural output of MEP calculation, continual indication is possible.
　/[IRC (out)] Reading the structural output of IRC calculation, continual indication is possible.
　/[Force] Reading the vibrational analysis result, infrared absorption spectrum indication and the indication of the vibration is possible.
[MOPAC parameter
　Set]		 The keyword column is replaced to the parameter for MOPAC.
[GAMESS parameter
　Set]		 The keyword column is replaced to the parameter for GAMESS.
[GAMESS start] The GAMESS input file is formed with present molecular keyword, to calculation can point.
[Edit out (log)] The standard output file of GAMESS (.out) You open with the designated editor.
[Import]
　/[Animation] The standard output file of GAMESS (.out) Reading, it indicates the coordinate change of optimization process.
　/[MO] The standard output file of GAMESS (.out) Reading, it indicates structure and the molecular track. Basis function, STO-3G and 3-21G (*), 6-31 (+) is limited to G (*) and 6-31G (d and p). Also 3D indication is possible.
[Gaussian parameter
　Set]		 The keyword column is replaced to the parameter for Gaussian.
[Gaussian start] The Gaussian input file is formed with present molecular keyword, to calculation can point.
[Edit log (out)] The output file of Gaussian is opened with the designated editor.
[Import]
　/[Import log (out)] Reading the structure of the output file of Gaussian, it indicates.
　/[Animation] The output file of Gaussian (.out) Reading, it indicates the coordinate change of optimization process.
　/[Opt] The output file of Gaussian (.out) Reading, it indicates optimization structure.
　/[MO] The output file of Gaussian (.out) Reading, it indicates structure and the molecular track. Basis function, STO-3G and 3-21G (*), 6-31 (+) is limited to G (*). Also 3D indication is possible.
[FormChk] Formchk of the Gaussian utility is started.
[CubeGen] Cubegen of the Gaussian utility is started, the Cube file which was drawn up is indicated.
[Import Cube] Reading the Cube type file, it indicates. Also 3D indication is possible.
[UNUX Server] Remote job control to the Linux (UNIX) machine with rsh and ftp. The execution control of Gaussian98/03 is possible. It corresponds to also LSF.
[CNDO/S parameter
　Set]		 The keyword column is replaced to the parameter for CNDO/S.
[CNDO/S start] CNDO/S calculation is executed.
Old JCPE which is registered to the Japanese computer conversion academic societyP083 (CNDO/S: Ultraviolet visible absorption spectrum calculation)（Manual) Is. With two programs as one, in order to be able to start from Winmostar, doing correction, compiling with g77 of Cygwin, cndosw.exe was drawn up. Source program (cndosw.f) Bundled it is done in the installation directory of Winmostar.
[UV-VIS [suhe] ゚ [kutoru] indication] The UV-Vis spectrum is indicated from CNDO/S output.
[Edit CNDO/S OutFile] The CNDO/S output file is opened.
[Molecular surface area cubic measure] Cubic measure and the surface area of the molecule are calculated. At this calculation has used the [hu] ゚ [roku] ゙ ram of Mr. Nagao of the Hakodate technical college.
　Bibliography) “Teruo Nagao revised Hakodate industrial technical college period main point of molecular surface area and cubic measure calculation program”
　　　(Hakodate Kogyo Koto Senmon Gakko Kiyo), 27th number, p111-120,1993
[MOLEKEL start] MOLEKEL is started.
[The home page of MOLEKEL] The download page of MOLEKEL is indicated.
[MOSF]
　/[MOSF parameter
　　　Set]		 The keyword column is replaced to the parameter for MOSF.
　/[MOSF start] MOSF calculation is executed.
　/[Editing MOSF
　　　File]		 The MOSF output file is opened with the designated editor.
[UV-VIS spectrum] The UV-Vis spectrum is indicated from MOSF output.
[Setting of pass] Pass of the executable file of various programs is appointed.


[In addition]
[Search] Various calculation result outputs keyword are searched, the line which is hit is designated as the Excel file.
[Continual execution] Calculation of the plural jobs of Gaussian and GAMESS is executed continually. High-class ones like the batch cuing/queuing system not to be the [te] (makes that may air does, but), it is something which it draws up & executes the bat file which is executed continually.
First, 1 molecular executions bat is possible by the fact that normally Gaussian and GAMESS are executed. After verifying that error does not appear in the execution time, in the DOS window [x] it ends.
[In addition]/[continual execution] with, 1 molecular execution bat files which have the fact that already it executed are indicated in the left side of the picture. As for file name input file name.It has become bat. When selecting the bat file> [=] you push, it is added to the right side of the picture. [Run] So, continual execution of the job which is set starts. [Run at] So, continual execution at the time when it appoints starts. As for continual execution job, winmos_batjob1 - 5.It is retained in bat. [Load] [Save] with also reading 込 retention is possible.
[Help]
[Manual] This manual is indicated.
[Home page] The home page of Winmostar is opened.
[Opinion, thought] One word please.
[Version information] Version information is indicated.

[Keyboard shortcut]
Superscription retention Ctrl+S
You reset to the origin Ctrl+Z
Atomic deletion F5
Element modification F4
Connection addition F6
Connection deletion F7
Enlargement F3
Reduction F2
Help F1
3-5 Modeling and MOPAC calculation of styrene

　The carbon of the molecular indicatory window is clicked in the initial screen, the button which is on top [- C6H5] is pushed when, structure of benzene is possible. When next, connects the hydrogen you want is clicked in the molecular indicatory window, [- C2H3] is pushed, the styrene is possible.
　From Calculation menu START When MOPAC6 is chosen, because the molecule was compiled, whether or not save it does, you hear. When here to be (Y) it chooses, the dos window appearing in the picture, calculation starts.
　That calculation, the Output file of the calculation result ends It is opened with text editor. When structural optimization calculation ends normally, the structure which is optimized in the molecular indicatory window is read automatically.
　When GRAPH keyword is appointed, molecular tracked indication is possible by the fact that the GPT file is read in calculation/molecular tracked indication.

3-6 Usage ofGAMESS

　As for GAMESS ab of free It is initio molecular orbital method [ha] ゚ [tsukeshi] ゙. It is transplanted in various [hu] ゚ rut/rat forms.
　Windows edition is WinGAMESS and PC-GAMESS.
　As for WinGAMESS,The formality HP of GAMESSThe empty it downloads. GAMESS (Contains all standard GAMESS options) ver. Xxx XX, 200X running ON Microsoft It is Windows.
　Downloading, it thaws WinGAMESS you can use directly, but as for PC-GAMESS, furthermore Dr. Alex A. The mail doing in Granovsky, it is necessary to inquire about the thawing password.
　Because WinGAMESS is something which [konha] ゚ [iru] is done with Cygwin, Linux edition and completely it is the same specification, but PC-GAMESS is a Linux edition and a part where specification differs.
　GUI for starting has belonged to WinGAMESS, but gamess.xx.When it passes through pass to exe, (calculation/setting /GAMESS of [ha] ゚ [su]) it can start even from Winmostar.
　From Calculation menu START It can execute with GAMESS. When you compare to MOPAC, because great calculation time is required, note you ask. Calculation is cancelled midway, [Ctrl] you push + [C].
　Like MOPAC in order for structure of the structural optimization result to be read automatically, it is not done. As for the structure which it optimizes［The reading of log 込] with it indicates.


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