Gabedit

Version 2.1.0
By Abdul-Rahman ALLOUCH Laboratoire de Spectromtrie Ionique et Molculaire - UMR 5579 CNRS et Universit Claude Bernard Lyon1

Copyright (C) 2002-2007 Abdul-Rahman ALLOUCHE

htt!"##$abedit.sour%e&or$e.net

Gabedit 'anual

Version 2.1.0

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Table of content
1) What is Gabedit? ................................................................................................................................... 3 2) Platforms ................................................................................................................................................. 3 3) Availability ............................................................................................................................................ 3 4) Citation .................................................................................................................................................. 4 5) Li ense ................................................................................................................................................... 4 !) "nstallation ............................................................................................................................................. 4 #) $etailed instr% tion for b%ildin& mole %le' reation of in(%t file and s%bmit a )ob *ith Ga%ssian' +ol as' +ol(ro' PCGamess' +P,C and ,-Chem............................................................ 6

7-1 Building Molecules ....................................................................................................................... 6 7-2 Creation of an input file for Gamess-US and PCGamess ............................................................. 7 7-3 Creation of an input file for Gaussian ......................................................................................... ) 7-4 Creation of an input file for Molcas ............................................................................................ * 7- Creation of an input file for Molpro ............................................................................................ + 7-6 Creation of an input file for MP!C ............................................................................................. 11 7-7 Creation of an input file for !-C"em ........................................................................................... 12 7-# Su$mit t"e %o$ ............................................................................................................................... 13 7-& 'isuali(ing t"e )esults ................................................................................................................. 14 'isuali(ing of or$itals* densit+ or ot"er ,from a cu$e file- .................................................... 1 'isuali(ing of dipole* .+( a.es and t"e principal a.es of molecule ...................................... 16 /nimation of 0i$ration ......................................................................................................... 17 /nimation of rotation ........................................................................................................... 17 /nimation of geometr+ con0ergence ..................................................................................... 1# /nimation of contours ........................................................................................................... 1# /nimation of planes colorcoded ............................................................................................ 1& .) /he Gabedit format 0.&ab) ...................................................................................................................... 21 1) /he Gabedit %be 2ormat 0.& %be) ........................................................................................................ 23 13) /%torial .................................................................................................................................................. 24

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1) What is Gabedit ?
Gabedit is a $ra!hi%al user inter&a%e to %om!utational %hemistry !a%,a$es li,e Gamess-U-. Gaussian. 'ol%as. 'ol!ro. '/0C /CGamess and 0-Chem 1t %an dis!lay a 2ariety o& %al%ulation results in%ludin$ su!!ort &or most ma3or mole%ular &ile &ormats. 4he ad2an%ed 5'ole%ule Builder5 allo6s to ra!idly s,et%h in mole%ules and e7amine them in 89. Gra!hi%s %an be e7!orted to 2arious &ormats. in%ludin$ animations.

Major features

Gabedit %an %reates in!ut &ile &or GA' --:U-;. GAU--1A<. 'OLCA-. 'OL/RO . '/0C /CGamess and 0-Chem. Gabedit %an $ra!hi%ally dis!lay a 2ariety o& Gamess-U-. Gaussian. 'ol%as. 'ol!ro. '/0C. /CGamess. 0-Chem and :!artially; A9= %al%ulation results. in%ludin$ the &ollo6in$ 'ole%ular orbitals. -ur&a%es &rom the ele%tron density. ele%trostati% !otential. <'R shieldin$ density. and other !ro!erties. -ur&a%es may be dis!layed in solid. translu%ent and 6ire mesh modes. they are %an be %olor%oded by a se!arate !ro!erty. Contours :%olor%oded;. /lanes %olor%oded. 9i!ole. >?@ a7es and the !rin%i!al a7es o& the mole%ule. Animation o& the normal modes %orres!ondin$ to 2ibrational &reAuen%ies. Animation o& the rotation o& $eometry. sur&a%es. %ontours. !lanes %olor%oded. 7yB and the !rin%i!al a7es o& the mole%ule. Animation o& %ontours. Animation o& !lanes %olor%oded. Gabedit %an dis!lay UV-Vis. 1R and Raman %om!uted s!e%tra. Gabedit %an $enerate a !o2ray &ile &or $eometry :in%ludin$ hydro$enCs bond;.sur&a%es :in%ludin$ %olor%oded sur&a%es;. %ontours. !lanes %olor%oded. Gabedit %an sa2e !i%ture in B'/. D/ G. /<G. //' and /- &ormat. Gabedit %an $enerate automati%ally a series o& !i%tures &or animation :2ibration. $eometry %on2er$en%e. rotation. %ontours. !lanes %olor%oded;.

2) Platforms
Gabedit is !retty mu%h !lat&orm inde!endent. U! to no6 1t has tested on Eindo6s:>/. 2000. Vista;. Linu7 :RedHat. 'andra,e. 9ebian;. 'a%O-> and U<1> :9i$ital 4RUF(. 4%n Ultra. 1B' A1>....; Gabedit is 6ritten in C and uses the $t,G and O!enGL :or 'esa89; libraries. /lease note " the 2.(.7 : or hi$her; 2ersion o& Gt,G is reAuired &or this 2ersion o& Gabedit. 4he $t,G and O!enGL:or 'esa89; $ra!hi%s libraries are a2ailable on many U<1> systems. L1<U> and also on E1<9OE-.

3) Availability
Gabedit is &ree. 4he sour%e &iles are a2ailable. /re%om!iled e7e%utable &iles are a2ailable &or Linu7. 'a% O>11 and Eindo6s systems.

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4) Citation
/lease use the &ollo6in$ %itations in any re!ort or !ubli%ation " A.R. ALLOUCH . Gabedit is a &ree Gra!hi%al User 1nter&a%e &or %om!utational %hemistry !a%,a$es. 1t is a2ailable &rom htt!"##$abedit.sour%e&or$e.net#

5) License
Co!yri$ht :C; 2002-200) Abdul-Rahman Allou%he . All ri$hts reser2ed /ermission is hereby $ranted. &ree o& %har$e. to any !erson obtainin$ a %o!y o& this so&t6are:the Gabedit; and asso%iated do%umentation &iles . to deal in the -o&t6are 6ithout restri%tion. in%ludin$ 6ithout limitation the ri$hts to use. %o!y. modi&y. mer$e. !ublish. distribute. subli%ense. and#or sell %o!ies o& the -o&t6are. and to !ermit !ersons to 6hom the -o&t6are is &urnished to do so. sub3e%t to the &ollo6in$ %onditions" 4he abo2e %o!yri$ht noti%e and this !ermission noti%e shall be in%luded in all %o!ies or substantial !ortions o& the -o&t6are. 4H -O=4EAR 1- /ROV19 9 5A- 1-5. E14HOU4 EARRA<4? O= A<? H1<9. >/R -- OR 1'/L1 9. 1<CLU91<G BU4 <O4 L1'14 9 4O 4H EARRA<41 - O= ' RCHA<4AB1L14?. =14< -- =OR A /AR41CULAR /UR/O- A<9 <O<1<=R1<G ' <4. 1< <O V <4 -HALL 4H AU4HOR- OR CO/?R1GH4 HOL9 R- B L1ABL =OR A<? CLA1'. 9A'AG - OR O4H R L1AB1L14?. EH 4H R 1< A< AC41O< O= CO<4RAC4. 4OR4 OR O4H RE1- . AR1-1<G =RO'. OU4 O= OR 1< CO<< C41O< E14H 4H -O=4EAR OR 4H U- OR O4H R 9 AL1<G- 1< 4H -O=4EAR .

!) "nstallation
F-1 ReAuirements O!enGL :or 'esa89; and $t,G.2.(.7 :or hi$her; libraries &or U<1>. <othin$ &or Linu7. 'a%O->11 and Eindo6s system. F-2 Un!a%, and install under Linu7 :and U<1>; system usin$ the sour%e &iles do6nload Gabedit210-r%.tar.$B &ile &rom htt!"##$abedit.sour%e&or$e.net# 7e%ute the &ollo6in$ %ommands" $unBi! Gabedit210-r%.tar.$B tar -72& Gabedit210-r%.tar %d Gabedit210-r% ma,e #$abedit F-8 Un!a%, and install under Linu7 system usin$ the binary &iles F-8-1 Gt,2G is installed in your system do6nload Gabedit20)Linu718*FGlib%28.$B &rom htt!"##$abedit.sour%e&or$e.net# 7e%ute the &ollo6in$ %ommands" $unBi! Gabedit210Linu718*FGlib%28.$B %! Gabedit210Linu718*FGlib%28 $abedit %hmod uG7 $abedit .#$abedit Gabedit 'anual Version 2.1.0 (#2(

F-8-2 Gt,2G is not installed in your system do6nload Gabedit210Linu718*FGlib%281n%ludin$G4HLib.tar.$B 7e%ute the &ollo6in$ %ommands" $unBi! Gabedit210Linu718*FGlib%281n%ludin$G4HLib.tar.$B tar -72& Gabedit210Linu718*FGlib%281n%ludin$G4HLib.tar %d Gabedit .#$abedit F-( Un!a%, and install under 'a%O->11 usin$ the binary &ile do6nload Gabedit20)'a%O->.tar.$B &ile &rom htt!"##$abedit.sour%e&or$e.net# 7e%ute the &ollo6in$ %ommands :under >11; " $unBi! Gabedit210'a%O->.tar.$B tar -72& Gabedit210'a%O->.tar %d Gabedit210'a%O->11 .#$abedit.sh F-I Un!a%, and install under Eindo6s system do6nload setu!Gabedit210.e7e &ile &rom htt!"##$abedit.sour%e&or$e.net# Cli%, to setu!Gabedit210.e7e &ile. 7e%ute the Gabedit.e7e !ro$ram

Gabedit 'anual

Version 2.1.0

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#) $etailed instr% tions for b%ildin& mole %le' reation of in(%t file and s%bmit a )ob *ith Gamess-54' Ga%ssian' +ol as' +ol(ro' +P,C' PCGamess and ,-Chem

)-1 Building Molecules

From the principal menu of Gabedit, select Geometr+23ra4. You can also click to 'Draw Geometry' icon ( ;. ?ou 6ill obtain a ne6 6indo6 :bla%, by de&ault;.

?ou %an use it to ra!idly s,et%h in mole%ules and e7amine them in three dimensions. =or this. Gabedit o&&ers 2arious !ossibilities " 1; ?ou %an read the stru%ture o& a mole%ule &rom a e7istin$ &ile. =or this usin$ the ri$ht button o& mouse. %li%, in dra6in$ area :bla%, by de&ault; and sele%t )ead. 2; ?ou %an build linear mole%ules. rin$ mole%ules. mole%ules 6ith an a7is o& symmetry. /oly!e!tides. /olynu%lei% a%ids. nanotubes. =or this %li%, on dra6in$ area :6ith ri$ht button o& mouse; and sele%t Build. 8; ?ou %an also build mole%ules &rom atoms or &ra$ments :=rom /dd25our 6ragment;. About 100 &ra$ments are at dis!osable in Gabedit. ?ou %an also %reate your !ersonal &ra$ments. (; ?ou %an modi&y the mole%ule in 89. =or this. =irst " -ele%t one or some atoms by usin$ i%on &or a &ree sele%tion or i%on &or sele%t a &ra$ment o& mole%ule. 4hese 2 i%ons are in the toolbar 6indo6 o& C9ra6 GeometryC 6indo6 :ri$ht-hand side o& this 6indo6;. ?ou %an use the -hi&t ,ey o& ,eyboard to sele%t se!arated &ra$ments. 4hen " - ?ou %an mo2e or rotate the sele%ted atoms by usin$ . or i%ons. <ote that you %an measure atom-atom distan%e. an$les and torsion an$les. =or this. %li%, to the i%on and sele%t &our atoms o& the mole%ule. Gabedit 'anual Version 2.1.0 F#2(

- 4o delete the sele%ted atoms %li%, to

i%on and %li%, on one o& the sele%ted atoms.

- 4o add:or re!la%e; an atom %li%, to i%on and sele%t the atom to be inserted :by %li%,in$ on i%on;. 4hen %li%, on dra6in$ area. 1& you ha2e %li%,ed on an atom. this atom is re!la%ed. I; ?ou %an o!timiBe the stru%ture by a 'ole%ular 'e%hani%s %al%ulation im!lemented in Gabedit. =or this. sele%t 'ole%ular Mec"anics27ptimi(ation8 -et your &a2orite !arameters and %li%, to OH button. F; ?ou %an run a 'ole%ular dynami% simulation by a 'ole%ular 'e%hani%s %al%ulation im!lemented in Gabedit. =or this. sele%t 'ole%ular Mec"anics2Molecular 3+namics8 -et your &a2orite !arameters and %li%, to OH button.

)-2 Creation of an input file for Gamess-US or PCGamess

Close the $eometry 6indo6. On the !rin%i!al toolbar. Cli%, to Gamess: use the !rin%i!al menu " 6ile29e4). ?ou 6ill obtain a ne6 6indo6. &or Gamess-U- or &or /CGamess; i%on :you %an also

4hen.

sele%t %har$e o& system and s!in multi!li%ity o& your system. sele%t your method :Run ty!e. -C= 4y!e. Correlation ty!e;. basis :BA-1- =rame;

A&ter %li%,in$ on the OH button. Gabedit $enerates the in!ut &ile and !uts this &ile in a te7t editor. ?our %an use the te7t editor to edit this &ile.

)-8 Creation of an input file for Gaussian

Close the $eometry 6indo6. On the !rin%i!al toolbar. Cli%, to Gaussian: ; i%on :you %an also use the !rin%i!al menu " 6ile29e42Gaussian :nput). ?ou 6ill obtain a ne6 6indo6.

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4hen. sele%t your method :' 4HO9 =rame;. basis :BA-1- =rame; and the ty!e o& %al%ulation :sin$le !oint or Geometry o!timiBation; :4?/ =rame;. A&ter %li%,in$ on the OH button. Gabedit $enerates the in!ut &ile and !uts this &ile in a te7t editor. ?our %an use the te7t editor to edit this &ile.

)-( Creation of an input file for Molcas Close the $eometry 6indo6.
On the !rin%i!al toolbar. Cli%, to 'ol%as: 6ile29e42Molcas;. ?ou 6ill ha2e a ne6 6indo6. ; i%on :you %an also use the !rin%i!al menu "

Gabedit dete%ts the symmetry o& mole%ule and the list o& atoms to insert in the in!ut &ile. Gabedit use de&ault toleran%e !arameters &or %om!ute the symmetry. By %li%,in$ on 4oleran%e button you %an %han$e these !arameters. Gabedit 'anual Version 2.1.0 *#2(

By de&ault Gabedit set the basis to -4O8G &or all atoms. ?ou %an %han$e this basis by %li%,in$ on -et Basis button. Choose the method :&rom the -C= /ro$ram &rame;. A&ter %li%,in$ on the OH button. Gabedit $enerates the in!ut &ile and !uts this &ile in a te7t editor. ?our %an use the te7t editor &or editin$ this &ile.

4o %hoose the basis &or an atom " -ele%t the atom &rom the le&t list. -ele%t the basis &or the sele%ted atom &rom the ri$ht list. =inally %li%, to OH button.

)-I Creation of an input file for Molpro

Close the $eometry 6indo6. On the !rin%i!al toolbar. Cli%, to 'ol!ro: ; i%on :you %an also use the !rin%i!al menu " 6ile29e42Molpro :nput;. ?ou 6ill obtain a ne6 6indo6.

Gabedit sets the $eneral !arameters to de&ault 2alues in 'ol!ro. ?ou %an %han$e these !arameters in this 6indo6. Cli%, to < >4 button. Gabedit 'anual Version 2.1.0 +#2(

?ou 6ill obtain a ne6 6indo6. In this window, you obtain the geometry (XYZ or Z-Matrix) of your molecule. By default no variables coordinates are defined. To define the coordinates (VARIABLES) to optimize for a geometry optimization : Click (with right button of the mouse) on the list of coordinates. To select the are to be changed in the optimization process. (In the example, they are XO5, YO5, ZO5, XO9, YO9, ZO9). You can also click (right button of mouse) on the list of VARIABLES for render fixed the selected ones. To modify the coordinates of an atom (or a variable) double click on this atom and modify. From the pop up menu (right button of mouse) you have also other utilities : sort, multiply by a0 , divide by a0, convert in Zmatrix (or in xyz ), draw your geometry... Click to !"# button. You will obtain a new window for choose the basis sets for the $arious atoms. 4o %hoose the basis &or an atom " - -ele%t the atom &rom the le&t list. - =rom the ri$ht list. -ele%t the C/ and#or the basis &or sele%ted atom.

Click to !"# button. You will %et a new window for choose the calculation methods.

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4o %hoose a method %li%, to the list o& the methods. a2ailable at the to! o& the 6indo6. 4o %han$e the de&ault !arameters o& this method. %li%, to buttons at the bottom o& the 6indo6. 4o add a &urther method. %li%, to the list o& methods :at to! o& the 6indo6;.

A&ter %li%,in$ on the =1<1-H button. Gabedit $enerates the in!ut &ile and !uts this &ile in a te7t editor. ?our %an use the te7t editor &or editin$ this &ile.

)-F Creation of an input file for MP!C Close the $eometry 6indo6.
On the !rin%i!al toolbar. Cli%, to '/0C: ?ou 6ill obtain a ne6 6indo6. ; i%on

-ele%t the $rou! symmetry. -ele%t the ty!e o& %al%ulation " sin$le !oint. o!timiBation :lo%al minimum or transition state;. Gabedit 'anual Version 2.1.0 11#2(

-et the !arameters :Char$e. multi!li%ity. method. basis...; used &or %om!utin$ the mole%uleCs ener$y. -et the !arameters :Char$e. multi!li%ity. method. basis...; used &or %om!utin$ $uess 6a2e &un%tion. -ele%t the !ro!erties to %al%ulate :atomi% natural orbitals. natural !o!ulations. &reAuen%ies;. A&ter %li%,in$ on the OH button. Gabedit $enerates the in!ut &ile and !uts this &ile in a te7t editor. ?our %an use the te7t editor &or editin$ this &ile.

)-) Creation of an input file for !-C"em Close the $eometry 6indo6.
On the !rin%i!al toolbar. Cli%, to 0-Chem: ; i%on. ?ou 6ill obtain a ne6 6indo6.

-et the !arameters. A&ter %li%,in$ on the OH button. Gabedit $enerates the in!ut &ile and !uts this &ile in a te7t editor. ?our %an use the te7t editor &or editin$ this &ile.

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)-* Su$mit a %o$8

Click to run ( ) icon. You will %et a new window. - Set the directory (Local Directory :). - Set the name of the input file (Save data in file :)

%li%, to OH button &or submit your 3ob.

A) Command for s%bmit a )ob

Gabedit set this %ommand to C$msC. Cnohu! $+*C. Cnohu! mol%asC . Cnohu! mol!roC and Cnohu! m!A%C &or Gamess-U-. Gaussian. 'ol%as. 'ol!ro and '/0C res!e%ti2ely. Ho6e2er you %an modi&y the de&ault 2alue &rom 4ettin&s6Preferen es o& the !rin%i!al menu o& Gabedit. 5nder Windo*s 7 "& you 6ant to use 6inGamess. you shoud set the 6inGamess dire%tory &rom -ettin$s#/re&eren%es. 1& you 6ant to use /CGamess. you shoud set the /CGamess dire%tory &rom -ettin$s#/re&eren%es. =or run Gamess-U- the de&ault %ommand is $amess.0I.e7e. 1& you 2ersion o& Gamess-U- is not 0I. you should re!la%e 0I by the number 2ersion o& your Gamess 2ersion. 5nder 5ni8 0Lin%8 or +a 94 :11) 7 i& you 6ant to use Gamess-U-. you should %han$e the C$msC and Crun$msC s%ri!ts o& Gamess-U- " 1n C$msC &ile " re!la%e line C.#run$ms JDOB JV R<O J<<O9 - KL JLOG=1L C by the 2 lines " set GA' --M1<-4ALLM91RNOdirname J0O JGA' --M1<-4ALLM91R#run$ms JDOB JV R<O J<<O9 - KL JLOG=1L 1n Crun$msC &ile re!la%e set G'-/A4HN.# by set G'-/A4HNOdirname J0O ?ou %an also use any %ommand 6ith any number o& !arameters but the last !arameter should be the name o& the in!ut &ile. 1n Gabedit#utils dire%tory. you ha2e se2eral e7am!les &or run Gamess-Us. Gaussian. 'ol%as. 'ol!ro and '/0C usin$ a bat%h system :/B9. L-= or LoadLe2eler bat%h system;. ?ou should be install the shell %ommand on your remote ser2er. dit the shell &ile and set the %orre%t 2alue o& !arameters 6hi%h %orres!ond to your Gamess-U-. Gaussian. 'ol%as. 'ol!ro or '/0C installation.

;) 4%bmit a )ob on a remote server

?ou %an submit your 3ob on your lo%al ma%hine :only on Linu7 and uni7 systems; or on a remote Gabedit 'anual Version 2.1.0 18#2(

ser2er. =or Eindo6s system. you %an not run Gaussian. 'ol%as. 'ol!ro and '/0C on your lo%al ma%hine. ?ou should submit your 3ob on a remote :Linu7 or Uni7; ser2er. =or submit your 3ob on a remote ser2er. you should %on&i$ure Gabedit to obtain the de&ault net6or, !roto%ol :rsh or ssh;. =or this. sele%t Settings2Preferences o& the !rin%i!al menu o& Gabedit and %li%, to C7t"erC Eindo6. 4hen sele%t your &a2ourite !roto%ol. -ele%t also your &a2ourite Bat%h system. & 6or 4indo4s s+stem ; you should select the pro%ram pscp and plink (these ' pro%rams are in Gabedit installation directory). You should e(ecute putty pro%ram (once is enou%h). &or add your ser2er on the list o& authoriBed ser2ers. & 6or linu.,and uni.- s+stem ) click to *elp button for obtain all the informations about the confi%uration of your system, confi%uration re+uired for bein% able to submit a ,ob on a remote ser$er. A&ter submittin$ your 3ob. you %an sho6 the list o& your 3obs on the remote ser2er :and ,ill a 3ob i& ne%essary;. =or this. sele%t <ools2Batc"2)emote2User &rom the !rin%i!al menu o& Gabedit.

-./ 'isuali(ing t"e )esults

-ele%t the noteboo, o& the out!ut &ile. - Cli%, to Update2end button. i& your 3ob is submitted on the lo%al ma%hine. - Cli%, to Get /ll &iles button. i& your 3ob is submitted on a remote ma%hine. - ?ou %an 2isualiBe the $eometry %on2er$en%e by %li%,in$ on the Geom8 Con0. Button. - Cli%, to 3ens8 7r$ button. &or 2isualiBe the orbitals. the ele%troni% density. ele%tri% di!ole or the 2ibration.

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'isuali(ing or$itals* densit+ or ot"er ;

A&ter %li%,in$ on the 3ens8 7r$. button :or on the you 6ill obtain a ne6 6indo6. i%on &rom the !rin%i!al toolbar o& Gabedit;.

- ?ou %an read orbitals &rom a " Gaussian out!ut &ile. 'ol!ro out!ut &ile. Gabedit &ile or 'olden &ile. =or this usin$ the ri$ht button o& mouse. %li%, in dra6in$ area :bla%, by de&ault; and sele%t 7r$itals &rom the !o! u! menu. Choose a ty!e o& &ile and the the &ile. A&ter readin$ the orbitals. you %an sele%t :you 6ill ha2e a 6indo6 6ith the list o& all orbitals; an orbital. ?ou %an also %al%ulate the ele%troni% density usin$ these orbitals : 9ensity# le%troni% &rom the !o! u! menu;. =or %hoose the iso2alue. sele%t Surfaces2resetiso0alue &rom the !o! u! menu. =or %reate a ne6 sur&a%e sele%t Surfaces2ne4 surface &rom the !o! u! menu. =or delete all sur&a%es sele%t Surfaces23elete /ll &rom the !o! u! menu. =or %hoose the ty!e o& sur&a%e. sele%t )ender2Surface &rom the !o! u! menu. ?ou %an use the rotation : . ;. Boom : ; and !ers!e%ti2e : ;i%ons. 4hen by mo2in$ the mouse 6hile holdin$ do6n the le&t button you %an obtain an o!timal ima$e. ?ou %an also obtain an o!timal ima$e by %li%,in$ on 5O5 button. ?ou %an also obtain an o!timal ima$e by settin$ the %amera !arameters. =or this sele%t Set2Camera &rom the !o! u! menu. =inally. you %an %reate a !o2ray &ile by sele%tin$ =.port2Po0ra+ &rom the !o! u! menu. =inally. you %an sa2e the ima$e on a B'/. //'. D/ G. /<G. or /- &ile by sele%tin$ Screen Capture &rom the !o! u! menu. - ?ou %an also read orbitals. density. ele%trostati% !otential. la!la%ian &rom a %ube &ile. 4he %ube &ormat &ile su!!orted by Gabedit are " Gaussian %ube &ile :orbitals. density. !otential. la!la%ian;. 'ol!ro %ube &ile:orbitals. density. !otential. la!la%ian;. Gabedit %ube &ile :see the last !a$e o& the manual;. A9= ta!e (1 :orbitals and density;. '2'-1 : A-C11 &ormat &rom 'ol%as so&t6are;. =or read a %ube &ile. sele%t Cu$e &rom the !o! u! menu. the %hoose the &ormat &ile. Eith Gabedit you %an also subtra%t $rid data &rom a &ile &rom the %urrently loaded data by sele%tin$ Cu$e2Su$tract &rom the !o! u! menu. - Eith Gabedit you %an also %reate an isosur&a%e %olor%oded 6ith another $rid. =or this " read :or %reate &rom orbitals; the $rid used to %olor the sur&a%e. -a2e this $rid in Gabedit %ube &ile. read :or %reate &rom orbitals; the $rid %olor%oded by the old $rid. =orm the !o! u! menu. sele%t Cu$e2Color Mapping and read the Gabedit %ube &ile. Gabedit 'anual Version 2.1.0 1I#2(

At the bottom o& the 9ra6in$ 6indo6. set the min and the ma7 2alues used to %olor the sur&a%e.

0hat this 1 0ater molecule, *232 orbital colorcoded with the electronic density. 4so$alue 5 6.7

'isuali(ing of dipole* .+( a.es and t"e principal a.es of molecule8

Gabedit read orbitals. $eometry and di!ole &rom the out!ut &ile o& Gaussian and 'ol!ro. Ho6e2er you %an set the 7. y and B %om!onents o& di!ole. =or this &rom the !o! u! menu sele%t Set23ipole and set your 2alues. ?ou %an also %han$e the %olor used &or dra6 the di!ole. ?ou %an also %om!ute the di!ole. numeri%ally. &rom the ele%troni% density " Set2Compute 3ipole from densit+. 4o sho6 7yB a7es. sele%t )ender2S"o4 >5? a.es :&rom the !o! u! menu;. 4o %han$e the %olor used &or dra6 these a7es. sele%t Set2>5? a.es properties8 4o sho6 the !rin%i!al a7es. sele%t )ender2S"o4 t"e principal a.es :&rom the !o! u! menu;. 4o %han$e the %olor used &or dra6 these a7es. sele%t Set2 t"e principal a.es properties8

Gabedit 'anual

Version 2.1.0

1F#2(

/nimation of 0i$ration ;
=rom the !o! u! menu sele%t /nimation2'i$ration. ?ou 6ill obtain a ne6 6indo6. 1) =rom the menu o& this 6indo6 :or &rom the !o! u! menu o& this 6indo6 obtain by %li%,in$:ri$ht button o& mouse; on the list o& &reAuen%ies;. %hoose the ty!e o& &ile to read. Eith Gabedit you %an read &reAuen%ies and the normal modes &rom" - a Gaussian out!ut &ile - a 'ol!ro ou!ut &ile - an A9=:2ersion 200(; out!ut &ile - a Gabedit &ile - a 'olden &ile 2) -ele%t a &reAuen%y &rom the list. 8; -et the 2alue o& Scale factor. <ime step. /rro4 radius and Steps $+ c+cle !arameters :i& ne%essary;. 3) By rotation and Boom &ind the o!timal ima$e. 4) Cli%, to Play button &or animate the 2ibration. 5) Cli%, to 4to( button &or sto! the animation. !) =or %reate a animated &ile. sele%t Create a series of ;+P ima&es and %li%, to Play button. A&ter one %y%le you %an sto! the animation. Usin$ %on2ert !ro$ram. you %an %reate a '<G or a G1= animated &ile &rom the B'/ &iles $enerated by Gabedit.

/nimation of rotation ;
=rom the !o! u! menu sele%t /nimation2)otation. ?ou 6ill obtain a ne6 6indo6. Choose the axis of rotation. By rotation and Boom. &ind the o!timal ima$e. Cli%, to Play button &or animate the rotation. ?ou %an also %reate an animated &ile &or this animation :see the 2ibration animation se%tion;.

Gabedit 'anual

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/nimation of geometr+ con0ergence ;

=rom the !o! u! menu sele%t /nimation2geometr+ con0ergence. ?ou 6ill obtain a ne6 6indo6. By rotation and Boom. &ind the o!timal ima$e. Cli%, to Play button &or start animation. ?ou %an also %reate an animated &ile &or this animation :see the 2ibration animation se%tion;.

/nimation of contours ;
=rom the !o! u! menu sele%t /nimation2Contours ?ou 6ill obtain a ne6 6indo6.

By rotation and Boom. &ind the o!timal ima$e. -ele%t the dire%tion. min iso2alue. ma7 iso2alue. and the number o& %ontours in ea%h !lane. -et the min and the ma7 2alue used &or %reate the %olorma! :On the bottom o& the le&t 6indo6;. Cli%, to Play button &or start animation. ?ou %an also %reate an animated &ile &or this animation :see the 2ibration animation se%tion;. Gabedit 'anual Version 2.1.0 1*#2(

/nimation of planes colorcoded ;

=rom the !o! u! menu sele%t /nimation2Planes colorcoded ?ou 6ill obtain a ne6 6indo6.

By rotation and Boom. &ind the o!timal ima$e. -et the min and the ma7 2alue used &or %reate the %olorma! :On the bottom o& the le&t 6indo6;. Cli%, to Play button &or start animation. ?ou %an also %reate an animated &ile &or this animation :see the 2ibration animation se%tion;.

Gabedit 'anual

Version 2.1.0

1+#2(

.) /he Gabedit 2ormat 0.&ab) Gabedit %an su!!ort any other !ro$rams 2ia the Gabedit &ormat. <ot all o& the belo6 se%tions are reAuired. you %ould ha2e PQAtomsR.QBasisR and Q'ORS . here QAOR is o!tional :this is used &or %al%ulate the di&&eren%e bet6een the ele%troni% density o& mole%ule and the ele%troni% density o& atoms;. Or P QG OCO<VR 6ith QG O' 4R1 -RS. Or P Q=R 0R.Q=R-COOR9R.Q=R-<OR'-COOR9R. here Q1<4R is o!tionalS =irst Line" <Gabedit 2ormat= 04(he > Cart) 4he 6or,in$s are 6ith -!heri%al or Cartesian Gaussian Basis &ormat. indi%ated by the -!he or Cart ,ey6ord.

Coordinates of Atoms for the Electron Density/Molecular orbitals:

[Atoms] (Angs|AU) element_name number atomic_number x y z ...

4he 6or,in$s are 6ith An$stroms or Atomi% Units. indi%ated by the An$s or AU ,ey6ord.

Specification of the basis-set consisting of contracted Gaussian Type Orbitals.

<;asis= atomMseAuen%eMnumber1 0 shellMlabel numberMo&M!rimiti2es 1.00 e7!onentM!rimiti2eM1 %ontra%tionM%oe&&i%ientM1 :%ontra%tionM%oe&&i%ientM1; ... em!ty line atomMseAuen%eMMnumber2 0 shellMlabel numberMo&M!rimiti2es 1.00 e7!onentM!rimiti2eM1 %ontra%tionM%oe&&i%ientM1 :%ontra%tionM%oe&&i%ientM1; ... em!ty line re%o$niBed shellMlabels" ?s?'?(?'?d?'?f?'?&?'?h?'?i?'?)?'?@?'?s(?' ?sd?' .... =or Cs!C. CsdC... shells t6o %ontra%tion %oe&&i%ients must be $i2en. &or both &irst and se%ond &un%tions. All 6or,in$s 6ith the <;asis= ,ey6ord are in Atomi% Units.

Specification of the molecular orbitals.

4he mole%ular orbitals and their o%%u!ation number are s!e%i&ied in the <+9= se%tion. =rom this in&ormation a density matri7 %an be %onstru%ted.
[MO] Sym= symmetry_label_1 Ene= mo_energy_1 Spin= (Alpha|Beta) Occup= mo_occupation_number_1 ao_number_1 mo_coefficient_1 ... ao_number_n mo_coefficient_n ....

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Sym= symmetry_label_N Ene= mo_energy_N Spin= (Alpha|Beta) Occup= mo_occupation_number_N ao_number_1 mo_coefficient_1 ... ao_number_n mo_coefficient_n

Specification of the atomic orbitals.

4he atomi% orbitals and their o%%u!ation number are s!e%i&ied in the <A9= se%tion. <A9= AtomN Atomi% -ymbolM1 4ymN symmetryMlabelM1 AneN aoMener$yM1 4(inN :Al!haTBeta; 9 %(N aoMo%%u!ationMnumberM1 aoMnumberM1 aoM%oe&&i%ientM1 ... aoMnumberMn aoM%oe&&i%ientMn .... AtomN Atomi% -ymbolMi 4ymN symmetryMlabelM< AneN aoMener$yM< 4(inN :Al!haTBeta; 9 %(N aoMo%%u!ationMnumberM< aoMnumberM1 aoM%oe&&i%ientM1 ... aoMnumberMn aoM%oe&&i%ientMn

Specification of frequencies and corresponding normal coordinates.

4he atomi% %oordinates 7.y.B and atomi% dis!la%ements d7.dy.dB are all in Bohr :Atomi% Unit o& len$th;. <2BA,= &reAuen%yM1 ... &reAuen%yMn <2B-C99B$= atomM1MelementMstrin$ 7 y B ... atomMnMelementMstrin$ 7 y B <2B-C9B+-C99B$= 2ibration 2ibrationMnumberM1 atomM1Md7 atomM1Mdy atomM1MdB ... atomMnMd7 atomMnMdy atomMnMdB .... 2ibration 2ibrationMnumberM< atomM1Md7 atomM1Mdy atomM1MdB ... atomMnMd7 atomMnMdy atomMnMdB <"C/= irMintensityM1 ramanMintensityM1 ... Gabedit 'anual Version 2.1.0 21#2(

irMintensityMn ramanMintensityMn

The Geometry Convergence section

4he ma7-&or%e. rms-&or%e. ma7-ste! and rms-ste! se%tions are o!tional. 4he atomi% %oordinates 7.y.B are in an$stroms unit. <GA9C9CD= ener&y $eometry1Mener$y ... $eometrynMener$y ma8-for e $eometryM1Mma7imumM&or%e ... $eometryMnMma7imumM&or%e rms-for e $eometryM1MrmsM&or%e ... $eometryMnMrmsM&or%e ma8-ste( $eometryM1Mma7imumMste! ... $eometryMnMma7imumMste! rms-ste( $eometryM1MrmsMste! ... $eometryMnMrmsMste! <GA9+A/B"A4= <umberMo&Matoms title or em!ty line :Geometry number 1; atomM1MelementMstrin$ 7 y B ... atomM:<umberMo&Matoms;MelementMstrin$ 7 y B ... ... ... <umberMo&Matoms title or em!ty line :Geometry number n; atomM1MelementMstrin$ 7 y B ... atomM:<umberMo&Matoms;MelementMstrin$ 7 y B

The Molecular Dynamics section Coord in An$. Velo%ity in AH'A. time in &s. ner$y in H%al#mol. residu<umberN0.1.2....
<+$= numberMo&M$eometries nAtoms time:&s; 4otal nery Hineti% ner$y /otential ner$y -ymbolM1 >M1 ?M1 @M1 V>M1 V?M1 V@M1 Char$e Amber4y!e /9B4y!e Residu<ame Residu<umber Gabedit 'anual Version 2.1.0 22#2(

...... -ymbolMn >Mn ?Mn @Mn V>Mn V?Mn V@Mn Char$e Amber4y!e /9B4y!e Residu<ame Residu<umber ...... ...... ....... nAtoms time:&s; 4otal nery Hineti% ner$y /otential ner$y -ymbolM1 >M1 ?M1 @M1 V>M1 V?M1 V@M1 Char$e Amber4y!e /9B4y!e Residu<ame Residu<umber ...... -ymbolMn >Mn ?Mn @Mn V>Mn V?Mn V@Mn Char$e Amber4y!e /9B4y!e Residu<ame Residu<umber

2inally' in the Gabedit6%tils6e8am(les dire tory yo% have 3 e8am(les files *ith Gabedit format. 4hese 8 &iles are also a2ailable on the Gabedit home !a$e " htt!"##$abedit.sour%e&or$e.net# 7am!les#e7am!leCarteBian.$ab htt!"##$abedit.sour%e&or$e.net# 7am!les#e7am!le-!heri%.$ab htt!"##$abedit.sour%e&or$e.net# 7am!les#e7am!leGeoCon2.$ab

1) /he Gabedit %be format 0.& %be)

4he &irst line is a %omment 4he se%ond line is a %omment
num b e rO&Atoms >-Ori$in ?-Ori$in @-Ori$in <1 >1 ?1 @1 # number of points, X, Y and Z of increments in the slowest running direction <2 >2 ?2 @2 <8 >8 ?8 @8 # number of points, X, Y and Z of increments in the fastest running direction @1 Ch$1 >1. ?1. @1 # Atomic number (integer), charge(real), and coordinates for each atom .... ....

:<1U<2; re%ords :len$th <8; 2alues of the density at each point in the %rid. ! a%h ro6 %ontain F reals
se!ar a te d by a bla%, s!a%e. 1&
8

is not a multi!le o& si7. then there may be blan, s!a%e in some lines.

A e7am!le o& a Gabedit %ube &ile " Grid &ile $enerated by Gabedit 9ensity 8 -(.000000 -(.000000 -(.000000 (0 0.20I12* 0.000000 0.000000 (0 0.000000 0.20I12* 0.000000 (0 0.000000 0.000000 0.20I12* * 0.000000 0.000000 0.000000 0.2IFI)F 1 0.000000 0.000000 1.(IF*88 -1.02F80( 1 0.000000 0.000000 -1.(IF*88 -1.02F80( -0.000000 -0.000000 -0.000000 -0.000000 -0.000000 -0.000000 -0.000000 -0.000000 -0.000000 -0.000000 -0.000001 -0.000001 -0.000001 -0.000001 -0.000002 -0.000002 -0.000002 -0.000008 -0.000008 -0.000008 -0.000008 -0.000008 -0.000008 -0.000008 Gabedit 'anual Version 2.1.0 28#2(

-0.000008 -0.000008 -0.000002 -0.000002 -0.000001 -0.000001 -0.000001 -0.000001 -0.000000 -0.000000 -0.000000 -0.000000 -0.000000 -0.000000 -0.000000 -0.000000 -0.000000 -0.000000 -0.000000 -0.000000 -0.000000 -0.000000 -0.000000 -0.000000 -0.000000 -0.000001 -0.000001 -0.000001 -0.000002 -0.000002 -0.000008 -0.00000( -0.00000( -0.00000I -0.00000F -0.00000F -0.00000F -0.00000F -0.00000F -0.00000F ...............................

13) /%torial
A tutorial &or Gabedit is a2ailable on the Gabedit home !a$e " htt!"##$abedit.sour%e&or$e.net#tutorial.html

Gabedit 'anual

Version 2.1.0

2(#2(