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Regards

Kazi

the different steps to run veda software are given below

All files generated by Veda program (.dd2; .mpo; .vdf; .ved; .log) are the text files.

All information about the action performed is to be written to the skra.log file.

VEDA is using the following Gaussian output files as its imput files: - log file named as: name1.log (or name1.out) - fch file (created from .chk file by the Gaussian utility program - utility option: formchk) named as: file1.fmu

The other manner of creation of the VEDA input is the following:

- extract form Gaussian .log file the information on the coordinates orientation, force constants (F-matrix) and frequencies with atom displacement matrix (ADM-matrix)

- save the extract as .fmt file (for VEDA4).

The F-matrix in log file should be preceded by the line: “Force constants in Cartesian coordinates”

The exemplary a1-91.fmt file is created in the above mentioned manner from the a1-91.log file of a 10-atoms molecule. By using the button “Create DD2” the VEDA4 program generates the skra.dd2 file which contents the following:

“Average coordinate population 1.000

s 1 1.00 STRE 4 7 NH 1.015024

s 2 1.00 STRE 2 1 CH 1.096447

s 3 1.00 STRE 2 5 CH 1.094347

s 4 1.00 STRE 6 8 CH 1.094349

s 5 1.00 STRE 2 3 CH 1.106690

s 6 1.00 STRE 6 9 CH 1.106696

s 7 1.00 STRE 6 10 CH 1.096447

s 8 1.00 STRE 4 2 NC 1.450644

s 9 1.00 STRE 4 6 NC 1.450631

s 10 1.00 BEND 7 4 6 HNC 109.30

s 11 1.00 BEND 1 2 3 HCH 107.21

s 12 1.00 BEND 5 2 1 HCH 107.42

s 13 1.00 BEND 8 6 10 HCH 107.42

s 14 1.00 BEND 3 2 5 HCH 108.14

s 15 1.00 BEND 9 6 8 HCH 108.13

s 16 1.00 BEND 10 6 9 HCH 107.20

s 17 1.00 BEND 6 4 2 CNC 112.81

s 18 1.00 TORS 7 4 2 1 HNCH -172.65

s 19 1.00 TORS 1 2 4 6 HCNC 65.52

s 20 1.00 TORS 5 2 4 6 HCNC -176.80

s 21 1.00 TORS 8 6 4 2 HCNC -183.20

s 22 1.00 TORS 3 2 4 6 HCNC -54.88

s 23 1.00 TORS 9 6 4 2 HCNC 54.88

s 24 1.00 TORS 10 6 4 2 HCNC -65.52

****

9 STRE modes:

1 2 3 4 5 6 7 8 9

8 BEND modes:

10 11 12 13 14 15 16 17

7 TORS modes:

18 19 20 21 22 23 24

19 CH modes:

2 3 4 5 6 7 11 12 13 14 15 16 18 19 20 21 22 23 24

0 USER modes:

...”

This is the introductory set of internal coordinates describing stretching, bending, and torsion movements (denoted as STRE, BEND, and TORS/OUT).

1. - "What are the exact meanings of the TORS and OUT descriptions in VEDA?"

TORS ABCD means the dihedral angle between the ABC and BCD planes

OUT ABCD means the angle between the AD vector and the BCD plane

In many cases the two definitions can describe the same atoms movement, but not always.

At the first stage of using VEDA, the most important is to start calculations with linearly independent set of coordinates. So use “Calculate” button to check whether the linear independence is satisfied or not. Note, that in coordinate definitions all information placed after the atom labels used for coordinate specification (two, three or four labels depend on coordinate type) plays only a comment role and can be neglected when the definition is edited.

2. -" What is the function of the "mix mode" key in the calculations? "

After the dd2 file is created, you can initially mix coordinates of the same type by using the

automatic mixing procedure (MIX button). It can influence the further optimization process.

After mixing (or not) press “Abandon mix mode” and make optimisation process (button “Optimize”). You can choose optimization options before mixing and change it during the optimisation. Some information on PED methodology you can find in the paper: M.H. Jamróz et al., Journal of Molecular Structure 787 (2006) 172–183).

Transformation of the normal modes into the internal modes, is based on molecular connectivity, results in non-diagonality of the force constant matrix expressed in the internal coordinates. Thus, the PED contributions of different modes are mutually dependent through the non-diagonal terms. So, redefinition of one of the internal coordinate to satisfy accepted constrains often damages the PED contributions of many other modes. Therefore a redefinition of the other coordinates is necessary. This is why the PED analysis needs to be repeated many times to obtain the maximized PED values and to achieve a reliable assignment. The above is performed in VEDA in the following way: The set of internal coordinates is replaced by an other set of coordinates and the PEDs are recalculated. A parameter (EPm) is introduced to express behavior of the set of PED values: it is the sum of the absolute values of maximal PEDs for each of the modes. Now, if after internal coordinate change the EPm parameter increases then the new set is accepted. This procedure we call the optimization of the PED analysis. Although, the program enables variation of the internal mode coefficients, they are conserved to be equal to 1. Numerically the whole problem increases as the number of combinations is increased and thus the PED optimization time increases rapidly with the number of modes.

Note, that if some of the coordinates (in the .dd2 file) are not clearly defined, you should try to edit that file. For example, delete some contributions in complex definitions and check if this do not disturb the quality of the analysis (do not decrease the coefficient remarkably). This is the "change-and-trial" method. Therefore, you have to do this separately for each coordinate. This is the main use of the EDIT key. After each change you have to reduce the whole set of coordinates using optimization ONLY with "Reduce coordinate" option, because a change in one coordinate usually causes a change of the properties of the other coordinates.

Using some keys from the “Control Box” you can influence the coordinate definitions and also can navigate the optimization process, for example by defining some user coordinate in .dd2 file and marking “hide coordinates USER/or NOT USER” in the control box you can optimize only the USER (or NOT USER) coordinates.

The a1-91a.dd2 file is the exemplary .dd2 file of the same 10-atoms molecule created by VEDA in the optimization course.

Note, that for large system the F-matrix in Cartesian coordinates is not placed in Gaussian log file. So, for such systems you should use the .chk file and generate the fch file by the Gaussian utility option: formchk.

The A1-91.fmu exemplary file is created from .fch (.fchk) file (it is sufficient to rename .fch to .fmu) The .chk (.fmu) file contains the F-matrix, but does not contain the ADM-matrix. So, to have full profit from VEDA analysis, there is a need to place the log file in the same folder with the same name as the .fmu file. For the A1-91 example it is sufficient to copy .fmt file to the .log file.

In the .vdf file, you can find the VEDA report on frequencies given in the Gaussian log file.

If there is a disagreement between the frequencies given in the Gaussian log and those calculated by VEDA larger than 0.5 cm-1, VEDA is labelling the appropriate frequency in the vdf by an asterix*). It is a 1:1 correspondence.

When the geometry is introduced from the log file, VEDA is reading the first encountered geometry. The geometry is reported in the VEDA log on the screen and also in the skra.log file.

The frequency disagreement will appear if a non-optimal geometry is introduced.

So, if geometry is read from the Gaussian log file, all the non-optimal “input/standard orientation” should be cut off. It is enough to replace “orientation” to “orien-tation”, for example.

It is additional reason to use .fmu file for reading the geometry (created from .chk file by the Gaussian program - utility option: formchk).

Some additional information you can find in VEDA4e.txt file.

When using the “View Structure” Option use:

left mouse (or shift-left mouse) for rotate the molecule

shift-right mouse to move the molecule

right mouse left-right direction to increase the molecule

right mouse up-down direction to increase the balls.