MacroModel Reference Manual - ISP

Chapter 4: Operation CodesMDFT — Molecular Dynamics Final TemperatureFinal Temperature (K, Absolute) to be achieved at end of run. The difference between the originalbath temperature (MDYN arg7) and the final desired temperature (MDFT arg5) is slowlysubtracted from the bath temperature over the course of the simulation. This temperaturechanging mechanism can be used to either heat or cool systems linearly during the simulation.The actual final temperature will be close but not equal to arg5. If a precise final temperature isdesired, a subsequent MDYN run with the desired temperature in MDYN arg7 should be used.MDYN arg7 and arg8 can also be used to heat or cool molecules over the course of a simulation.This alternative would be effected by having an initial temperature as desired and the finaltemp as MDYN arg7 and weak coupling to the temperature bath via MDYN arg8.arg5Temperature (K)0 MDFT inactive.Values less than 0.0001 K are not allowed.MDMC — Molecular Dynamics / Monte Carlo mixed modeMCSD — Monte Carlo / Stochastic Dynamics mixed modeThese commands are synonyms; MCSD is the preferred form, since its name reminds the userthat the mixed-mode procedure should always be carried out using stochastic dynamics. This isbecause stochastic dynamics and the Monte Carlo procedure both generate the canonicalensemble, whereas (constant-energy) molecular dynamics generates the microcanonicalensemble.This procedure mixes stochastic dynamics and Monte Carlo (MC) internal coordinate movements.This makes it possible to explore conformational (phase, configurational) space moreeffectively than dynamics alone, while using the dynamics paradigm to obtain free energies.Internal coordinate Monte Carlo movements must be specified using MOLS and TORScommands as is done in MCMM conformational searching. TORS commands involving ringbonds and RCA4 commands are allowed with MCSD, but the acceptance ratio is very low. If thiscombination of commands is used, DEBG 104 should be given.This command should only be used with stochastic dynamics (MDYN arg3=1 and arg7 !=0).We do not recommend using SHAKE (controlled via arg2 of MDYN) during MC/SD simulations,as its use can result in less than optimal temperature control. Using MCSD withoutSHAKE sometimes requires a smaller simulation timestep than might otherwise be used. Butsince MCSD is very efficient at exploring conformational space relative to dynamics alone, thisshould not be an issue.MacroModel 9.7 Reference Manual 127