Dialog box

Be careful when you use the Orbital Criterion for symmetrical system s. To get correct resnlis, you in u st include all or none of any set of degenerate orbitals in the Cl, n ot jn si some of them. Carrying out an RIIF calculation first and studying the Orbitals dialog box will help you to spot degenerate orbitals and avoid this pitfall. 

HyperChem tjuantum tn ech an ics calcu lation s tn ust start with the number of electrons (N) and how many of them have alpha spins (th e remain in g electron s have beta spin s ). HyperCh em obtain s th is in form ation from the charge an d spin m u Itiplicity th at you specify in th e Sem i-em pirical Op lion s dialog box or. Ab Initio Option s dialog box. is th en computed by coun ting the electron s (valence electrons in sem i-em pirical methods and all electrons in a/ irti/io m ethod) associated with each (assumed neutral) atom and... 

Run a molecular dynamics simulation, Start another simulation with the same molecular system and with Restart off in the Molecular Dynamics dialog box. HyperCheni assigns a new set of velocities at random. ... 

Snapshots at regular time intervals that store atomic coordi-riaies and velocities. You can play back these snapshots to inspect the simulated structures or to average values. Yon specify a Snapshot period in the Molecular Dynamics Snapshots dialog box. 

Tor all restraints, HyperChem uses named selections that contain two, three, or four atoms each. You use Name Selection on the Selectmenn to assign nam es to groups of selected atom s. Th en you can apply named selections as restraints for a calculation in the Restraint Forces dialog box from Restraints on the Setup menu. 

Before run ti in g a molecu lar dyn am ics sim ulatioti with solvent and a m olccular median ics meth od, choose the appropriate dielectric con Stan i. You specify th e type an d value of th c dielectric con slari t in thehorce hield Option s dialog box. ITi e dielectric con star t defines the screen irig effect of solvent molecules on nonbonded (electrostalic) in teraction s. 

Before startiu g a in olecular dyri am ics simulation, L-click on Averages in the Molecular Dynamics Option s dialog box. 

I o sorn c ex ten t you can rn on itor eon stan t tern peratii re sim ula-tion s by th e tern perature (I KMP) an cl its deviation (D TKM P) or by kinetic en ergy (KKIN) an d its deviation (D HKIN). Plot th ese values using the HyperChem Molecular Averages dialog box. 

You can restrain atom s dur ing m olecu lar m ecli an ics or quart tu in mceh an ies calculation s, Cli oosiri g restrain ts, via the Restrain t Horces dialog box, applies additional h arm on ie forces which you specify, to in teratorn re distari CCS, an gles, or dihedrals that you have set up as named selections. 

Certain option s are needed to setup lor running qiian turn mechanics calculations in IlyperChem via the corresponding option dialog boxes on the Setup menu. 

Specify the extra (net) charge and the spin multiplicity in the Ab In itio Options dialog box,... 

Sped fy th e extra (n ct) eh arge and spin rn iiltiplicily in the Seni i-etnpirical Options dialog box. 

After you select a method for a semi-empirical calculation (using the Semi-empirical item on the Setup menu l, choose Optionsm the dialog box to set conditions for the calculation. You sec the Semi-empirical Options dialog box. Th e I ollowmg section s explain th esc option s. 

Specify the charge and spin multiplicity in the Semi-empirical Option s dialog box. 

This dialog box also contains the option for specifying that the molecular system ism the first excited singlet stale (Next lowest or the Lowest electronic state. 

IlyperChetn displays the electrostatic potential as a contour plot when you select th e appropriate option in th e Con tour Plot dialog box. Choose the values for the starting contour and the contour increment so that you can observe the minimum (typically about 0.5 for polar organ ic molecules) and so that the zero potential line appears. 

IlyperChem avoids th e discon tin nily an d, in isotropy problem of th e implied cutoff by iin posing a sin oothed spherical cn toff within the implied cutoff. When a system is placed in a periodic box, a switched cnLoITis aiitoinatically added. The default outer radius, where the interaction is completely turned off, is the smallest of 1/2 R., 1/2 R.. and 1/2 R, so that the cutoff avoids discontinuities and is isotropic, fh is cutoff may be turned off or modified in the. Molecular Mechanics Options dialog box after solvation and before calcii lation. ... 

Use Restraints in the Setup menu to bring up the Restraint Forces dialog box... 

These molecular dynamics restraints are stored with the IIIX file and are relained as long as ihe Named Seleclions are slill active (structural changes not made to molecular systemli or the restraints are still rec iiested via the Restraint Forces dialog box. 

You can use Lhe senii-empineal an tl ab initio Orbuals dialog box in IlyperChem Lo ret iies[ a con Lour ploL of any molecular orbital. When req nested, lhe orbital is con toured for a plane that is parallel lo lhe screen and which is specified by a subset selection and a plane offset, as described above. The index of the orbilal and its orbilal energy (in electron volts, eV) appears in the stains line. 

HyperChem run s the molecular dynain ics trajectory, averaging and analyzing a trajectory and creating the Cartesian coordinates and velocities, fhe period for reporting these coordinates and velocities is th e data collection period. At-2. It is a m iiltiplc of the basic time step. At = ii At], and is also referred to as a data step. The value 1I2 is set in the Molecular Dynamics options dialog box. 

TlyperCi hem updates the screen diirin g a trajectory at regular in ter-vals so yon can visiiali/e the irajectory. Since this screen update may slow down a trajectory If it occurs too frequently, yon c.an specify the duration of the Screen Refresh period At.,. The screen updates at ilines tQ, Iq + Atj, to + 2Atj, etc. The Screen Refresh period is specified in the Molecular Dynamics options dialog box by n 5 data steps, i.e. as a m iiliiplc of the data collection period, At5 = n 5 At2-... 

---