Concise Physical Chemistry

c19 JWBS043-Rogers September 13, 2010 11:29 Printer Name: Yet to Come

314 CLASSICAL MOLECULAR MODELING

PROBLEMS AND EXAMPLES

Example 19.1 A Geometric Optimization of Water

Construct an input file for the MM4 geometry optimization of water.

Solution 19.1 First and most obvious, we name the molecule and enter the number

of atoms. In MM4, the name goes on line 1 and can occupy up to 60 columns (spaces).

In this case, we enterwaterin columns 1 to 5 of the first line in File 19.1 and specify

the number of atoms as 3 in column 65. On the second line or “card,” the number

0 in column 5 shows that there are noconnected atoms(see Example 19.3). The 2

in column 30 gives the number ofattached atoms, namely the two hydrogens. Line

3 identifies he attached atoms. Atom 2 (oxygen) is attached to atom 1 (one of the

hydrogens), and atom 2 (oxygen) is also attached to atom 3 (the other hydrogen)

Next, we input a starting geometry in Cartesian coordinates for all the atoms in the

molecule. The geometry chosen is a simple angle>with oxygen at the origin. The

position vectors of the two hydrogens in an arbitrary Cartesian coordinate space are

(−0.5, 0.5, 0.0) and (−0.5,−0.5, 0.0). The input geometry has been constrained to

thex, yplane by setting thezcomponents to zero. The Cartesian coordinates are given

in the orderx,y, andzfrom left to right. The O atom has an identifying number 6,

and the two hydrogens are given the number 21 in this MM4 convention. Numerical

identifiers are used to represent atoms, which may be of different kinds—for example,

sp,sp^2 ,orsp^3 carbon atoms. These two parts, the descriptive cards and the Cartesian

geometry, constitute the input file. Save your input files ash20.mm4or some similar

name with the suffix .mm4. It is to be emphasized that this is only one of very many

possible input files.

Example 19.2 A Typical Small Molecule Run

Run the MM4 input file, File 19.2. The run is initiated by typingmm4followed by

the input filenameh20.mm4.Enter 0 forparameters,1fortheline number,

and 2 for theprogram choice. Several alternatives are offered. Running them

later should make most of the differences self-evident.

Solution 19.2 A successful run should give a small steric energy of<1 kcal mol−^1.

Hit enter three times to exit MM4 and to save TAPE4.MM4 and TAPE9.MM4. Enter

water 3

0 2 0000000

212 3

-0.50000 0.50000 0.00000 21

0.00000 0.00000 0.00000 6

-0.50000 -0.50000 0.00000 21

FILE 19.2 An input file for water. The geometry is an arbitrarily chosen estimate. The zeros

in line 2 and in the Cartesian coordinates are only place indicators to make counting the

columns easier in more complicated files (see File 19.4).