Forcefield-Based Simulations.pdf

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1、1Contents1.Introduction1Whoshouldusethisdocumentation2Whatcansimulationenginesdo?2Energyminimization2Moleculardynamics3Otherforcefield-basedcalculations3Whatareforcefieldsandsimulationengines?4Usingthisguide5Additionalinformation6Typographicalconventions72.Forcefields

2、9Thepotentialenergysurface10Empiricalfittothepotentialenergysurface11Theforcefield12Theenergyexpression16ForcefieldssupportedbyMSIforcefieldengines19Maintypesofforcefields20Advantagesofhavingseveralforcefields23PrimaryusesofeachMSIforcefield24Second-generationforcefie

3、ldsaccurateformanyproperties26CFF91,PCFF,CFF,COMPASS—consistentforcefields28MMFF93,theMerckmolecularforcefield34Rule-basedforcefieldsbroadlyapplicabletotheperiodictable35ESFF,extensiblesystematicforcefield36UFF,universalforcefield42VALBOND44Dreidingforcefield51Classic

4、alforcefields53AMBERforcefield53CHARMmforcefield56CVFF,consistentvalenceforcefield57Special-purposeforcefields61Forcefield-BasedSimulations/September1998i1.ContentsGlassforcefield62MSXXforcefieldforpolyvinylidenefluoride64Zeoliteforcefields65Forcefieldsforsorptiononze

5、olites67ForcefieldsforCerius2•Morphologymodule67Archivedanduntestedforcefields683.PreparingtheEnergyExpressionandtheModel73Usingforcefields75Selectingforcefields78Assigningforcefieldatomtypesandcharges78Whatareatomtypesinforcefields?79Assigningatomtypestoamodel79Assig

6、ningcharges81Parameterassignment84Determinationofwhichparametersareusedwithwhichatomtypes84Automaticassignmentofvaluesformissingparameters86Manualparameterassignment89Usingalternativeformsofenergyterms92Removingtermsfromtheenergyexpression93Scalingoreditinganyselected

7、typeofterm94Alternativebondterms94Scaledtorsionterms95Inversionterms96Nonbondfunctionalform96Hydrogenbondsandhydrogen-bondterms96Bond–anglecrosstermsvs.Urey–Bradleyterms98Applyingconstraintsandrestraints98Whentouseconstraints/restraints100Fixedatomconstraints102Templa

8、teforcing,tethering,quarticdropletrestraints,andconsensusconformations103Generalinternal-coordinaterestraints106DistanceandN