Terns

Reduce stress on molecules caused hy a simulation at elevated tern peratiires. The cooling process, called sim n lated annealing, takes new, high energy conformational slates toward stable conformations. 

High tern perature sim ulation s requ ire special con sideratiori ir choosing the sampling interval (see Step size" on page 89),... 

Kinetic energy (EKfX i Potential energy (KPO I ) Total energy (ETOT) Tern perature (THMP)... 

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. 

For constant energy simulations without temperature regulation, use heating steps of about 0.5 ps and a healing time of 20-30 ps. In gen eral, short h eating tim es and large temperature steps perturb th e initial system m ore than Ion gcr heating times and small tern -perature steps. 

Tiiinpiiraiiii (3 is handled the sanii way in Langavin dynamics as it iisin molecular dynamics. High tern peraLurc runs m ay he n sed to overcome poten lial cnergy barriers. Cooling a system to a low tern -peratnre in steps may result in a different stable conformation than would be round by direct geometry optimization. 

The heating phase is used to take a molecular system smoothly from lower tern peratiires, indicative of a static initial (possibly optim i/ed ) structure, to th e temperature T at which it is desired to perform the molecular dynamics simulation. The run phase then consLitn tes a sim n lation at tern peratnre T. If th e heating h as been done carefully, it may be possible to skip the equilibration phase... 

In the heating phase (assuming i j is non-zero), the velocities are periodically rescaled to change the system temperature from the initial tern perature T to the simulation temperature T2 in incrc-m eiiis of th e temperature step AT. Th e h eaiin g period for rescaling the velocities, P, is defined by ... 

If th e Con Stan t tern peraLu re option h as n ot been selected, HyperCh cm s m oiccu lar dyn am ics uses con stan t volum e an d con -slant total energy corresponding to a rn icrocanon ical enscmhle. 

Coordin ates of atom s can he set by n orm al translation orrotation of HyperCh cm molecules, fo set initial velocities, however, it is necessary to edit th e H l. file explicitly. The tin it o f velocity in the HIN file is. An gstrom s/picosecon d.. Areact.hin file and a script react.scr are in eluded with HyperChem to illustrate one simple reacting trajectory. In order to have these initial velocities used in a trajectory the Restart check box of the Molecular Dynamics Option s dialog box must he checked. If it is n ot, the in itial velocities in the HIN file will be ignored and a re-equilibration to the tern peratiire f of th e Molecular Dyn am ics Option s dialog box will occur. This destroys any imposed initial conditions on the molecular dynamics trajectory. 

If Lh c con Stan t Ictn pcratti re a Igori Lli rn is used in a trajectory analysis, then the initial conditions arc constantly being modified according to the sirn ulation of th c con stan t tern perattirc bath an d th e relaxation of th e m olecu lar system to that bath temperature, fhe effect of such a bath on a trajectory analysis is less studied than for th c sirn 11 lation of cqu i libriii m behavior. 

The ratio of the two terns on the right hand side of equation (10.17) is... 

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