CHARMM Element doc/pressure.doc 1.3#File: Pressure, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax Constant Pressure/Temperature (CPT) Dynamics Two types of constant pressure/temperature dynamics are available in CHARMM. The weak coupling method for temperature and pressurecontrol described in the paper by Berendsen et al. (JCP 81(8) p36841984) was the first constant pressure and temperature algortihmimplemented in CHARMM. Extended system constant pressure and temperature algorithms have now been implemented based on the workof Andersen (JCP 72(4) p2384 1980), Nose & Klein (Mol Physics 50(5)p1055 1983), Hoover (Phys. Review A 31(3) p1695 1985). Additionally,a variant on the extended system method which treats the control variables by means of a Langevin equation is available (Feller, Zhang,Pastor & Brooks, JCP, 103, 4613 (1995)). Shape matrix propagation and coordinates scaling for triclinicunit cell is done according to D. Brown and J.H.R. Clarke inComputer Physics Comm. 62 (1991) 360-369. A constant surface tension algorithm is included which is usefulfor studying interfacial systems where one wishes to allow the areato change dynamically during the simulation. The dynamical equationsand statistical ensemble are discussed in (Zhang, Feller, Brooks & Pastor, JCP, 103, 10252 (1995)).* Menu:* Syntax:: Syntax of the CPT dynamics command* Description:: Description of the keywords and options* Notes:: Other points to be noted* Examples:: Isotropic and interfacial systems; constant tensor* Pressure:: The pressure command#File: Pressure, Node: Syntax, Up: Top, Next: Description, Previous: Top[Syntax DYNAmics CPT]DYNAmics CPT ... cpt-speccpt-spec::= [ pressure-spec ] [ temperature-spec ] [ surface-tension-spec ]pressure-spec::= PCONST {[PINTernal]} {BEREndsen berensen-spec} ref-pressure-spec { PEXTernal } { langevin-piston-spec }temperature-spec::= { TCONst [TCOUpling real] [TREFerence real] } ! Berendsen { } { HOOVer [TMASs real] [ REFT real] } ! Hooverberensen-spec::= [COMPressibility real] [PCOUpling real]langevin-piston-spec::= piston-mass-spec [PGAMMA real] [TBATH real]surface-tension-spec::= [SURFace] [TENSion real] piston-mass-spec::= [PMASs real] [PMXX real] [PMYY real] [PMZZ real] [PMXY real] [PMXZ real] [PMYZ real]ref-pressure-spec::= [PREFerence real] [PREFInitial real] [PREFFinal real] [PRXX real] [PRYY real] [PRZZ real] [PRXY real] [PRXZ real] [PRYZ real][PIXX real] [PIYY real] [PIZZ real] [PIXY real] [PIXZ real] [PIYZ real] [PFXX real] [PFYY real] [PFZZ real] [PFXY real] [PFXZ real] [PFYZ real] [VOLUME real] #File: Pressure, Node: Description, Previous: Syntax, Up: Top, Next: Notes Description of CPT Dynamics Commands Only a few changes are needed to a standard CHARMM dynamics inputfile to run a CPT MD simulation. There are a few things to note :a. The CPT algorithm is invoked by the CPT keyword.b. It's not possible to use LANGEVIN dynamics with the constant pressure or temperature algorithm. c. All the non-Langevin dynamics keywords have the same meaning as the in a standard dynamics input file. This includes the keywords STRT and REST.e. The CPT specific keywords (apart from CPT itself) are : 1. PCONstant - do a constant pressure calculation. Extended system algorithm is the default, weak-coupling is available with BEREndsen keyword. 2. TCONstant - do a constant temperature calculation with the weak- coupling algorithm. HOOVer constant temperature is only available with PCONstant simulations.f. The CPT module is only available for use with the leap-frog integrator 3. To be used with Berendsen algorithm: COMPressibility <real> - the isothermal compressibility (atmospheres**-1). PCOUple <real> - the pressure coupling constant (picoseconds). To be used with extended system algorithm: PMASs <real> - the mass of the pressure piston (amu) PGAMma <real> - Langevin piston collision frequency (1/ps) TBATh <real> - Langevin piston bath temperature TENSion <real> - reference surface tension (dyne/cm) To be used with either constant pressure algorithm: PREFerence <real> - the reference pressure (atmospheres). (for isotropic pressure) PREFInitial <real> - initial reference pressure tensor (atmospheres). (for isotropic pressure) PREFFnitial <real> - final reference pressure tensor (atmospheres). (for isotropic pressure) PRXX,PRYY,PRZZ <real> - the reference pressure tensor (atmospheres). PRXY,PRXZ,PRYZ (for anisotropic pressure) PIXX,PIYY,PIZZ <real> - initial reference pressure tensor (atmospheres). PIXY,PIXZ,PIYZ (for anisotropic pressure) PFXX,PFYY,PFZZ <real> - final reference pressure tensor (atmospheres). PFXY,PFXZ,PFYZ (for anisotropic pressure)PREFI,PREFF,PIXX...,PFXX... - are used for linear pressure ramping 4. To be used with Berendsen algorithm TCOUple <real> - the temperature coupling constant (picoseconds). TREFerence <real> - the berendsen reference temperature (K). To be used with extended system (HOOVer) algorithm TMASs <real> - the mass of the thermal piston (kcal*ps^2). REFT <real> - the hoover reference temperature (K). Note : for full descriptions of these parameters and the suggested values to use see the reference given above.#File: Pressure, Node: Notes, Up: Top, Previous: Description, Next: Examples Other PointsSuggested values for solvated systems: COMPressibility (beta) = 4.63e-5 /atm (for proteins) PCOUple = 5.0 ps (or more) PREF = 1.0 atm (default) PMASs = 500 amus (default is infinity) TCOUPle = 5.0 ps (or more) TREF = 298.0 K (default) REFT = 298.0 K (default) TBATh = 298.0 K (default) TMASs =