CHARMM Element doc/mc.doc $Revision: 1.6 $#File: mc, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax Monte CarloThe Monte Carlo commands in CHARMM have been designed to allow construction and use of an almost arbitrary move set with only a few atom selections. This goal is accomplished by providing a pre-defined set of move types which can be combined to specify the allowed movements of an arbitrary CHARMM molecule. Speed and flexibility are gained by separating the bookkeeping associated with a move (MOVE subcommands) from the actual application of that move to the molecule (MC).* Menu:* Syntax:: Syntax of MOVE and MC commands* Description:: Description of MOVE and MC commands* Examples:: Examples of MOVE and MC commands* Data Structures:: Data structures shared by the MOVE and MC commands* Shortcomings:: Known problems and limitations* References:: Some references of use#File: mc, Node: Syntax, Up: Top, Next: Description, Previous: Top Syntax for MOVE and MC commands[Syntax MOVE < ADD | DELEte | EDIT | READ | WRITe | LINK > ]MOVE ADD 1{ MVTP move-type } nsele{ SELE...END } - [ WEIGht 1.0 ] [ DMAX 1.0 ] [ TFACtor 1.0 ] - [ FEWEr 0 ] [ NLIMit 1 ] [ LABEL move-label ] - [ opt-spec ] [ mini-spec ] [ hmc-spec ] where nsele, the number of SELE...END statements, depends on move-typemove-type (nsele)::= < RTRN rig-unit ( 1 ) | ! Rigid translations RROT rig-unit ( 1+) | ! Rigid rotations CART ( 1 ) | ! Single atom displacements TORS ( 2 ) | ! Simple torsion rotations CROT [PIMC] ( 1+) | ! Concerted torsion rotations HMC ( 1 ) | ! Hybrid Monte Carlo VOLU rig-unit ( 1 ) > ! Volume scalingsrig-unit ::= < BYREsidue | BYALl | BYHEavy | BYATom >opt-spec ::= [ ARMP -1.0 ] [ ARMA 0.0 ] [ ARMB 0.0 ] - [ DOMCf -1.0 ] [ ANISotropic 0 ] mini-spec::= [ MINI < SD (default) | CONJ > ] - [ NSTEps 0 ] [ NPRInt 0 ] [STEP 0.2 ] - [ TOLEner 0.0 ] [ TOLGrad 0.0 ] [TOLStep 0.0 ] - [ INBFrq -1 ] hmc-spec ::= [ NMDSteps 0 ] [ TIMEstep 0.0 ] MOVE DELEte < MVINdex move-index | LABEL move-label > -MOVE EDIT < MVINdex move-index | LABEL move-label > - [ WEIGht prev ] [ DMAX prev ] [ TFACtor prev ] - [ NLIMit prev ] [ opt-spec ] [ mini-spec ] - [ hmc-spec ]prev ::= previous valueMOVE WRITE [UNIT -1]MOVE READ [UNIT -1] [APPEnd 1]MOVE LINK < MVI1 move-index | LAB1 move-label > - [ MVI2 move-index ] [ LAB2 move-label ] [Syntax MC]MC [ NSTEps 0 ] [ ISEEd prev ] [ IACCept 0 ] [ PICK 0 ] - [ TEMPerature 300.0 ] [ PRESsure 0.0 ] [ VOLUme prev ] [ ACECut 0.01 ] - [ INBFrq 0 ] [ IMGFrq 0 ] [ IECHeck 0 ] - [ IUNCrd -1 ] [ NSAVc 0 ] [ IMULti -1 ] - [ RESTart ] [ IUNRead -1 ] [ IUNWrite -1 ] - [ IARMfrq 0 ] [ IDOMcfrq 0 ] #File: mc, Node: Description, Up: Top, Next: Examples, Previous: Syntax MOVE The MOVE subcommands are associated with construction of the move set. The primary MOVE subcommand is MOVE ADD, which determines all of the locations in a subset of atoms to which a move type can be applied. For each location (or "move instance"), MOVE ADD also determines the rotation axes and centers, the moving atoms, and the relevant bonded terms. Thus, each call of MOVE ADD results in a group of move instances of the same move type (the number of instances is stored in the substitution variable ?NMVI). By repeatedly calling the MOVE ADD command, the user can employ several different types of moves in conjunction, which typically yields the most efficient and complete sampling. The available pre-defined move types are rigid translations (RTRN), rigid rotations (RROT), single atom displacements (RTRN), rotations of individual torsions (TORS), concerted rotation of seven (or, in the case of a chain end, six) torsions (CROT) to deform the system locally (Dinner, 2000; Dinner, 1999; Go and Scheraga, 1970; Dodd et al., 1993; Leontidis et al., 1994), hybrid Monte Carlo propagations (HMC) (Duane et al., 1987; Mehlig et al., 1992),and volume scaling moves for constant pressure simulations (Eppenga and Frenkel, 1984). Each of these can be applied to an arbitrary subset of atoms using standard CHARMM SELE...END statements. MVTP rig-unit nsele Description ---- -------- ----- ----------- RTRN BYALl 1 The entire atom selection is rigidly translated. RTRN BYREsidue 1 The residue containing each selected atom is rigidly translated. If more than one atom in a residue is selected, each counts as a separate move instance. RTRN BYHEavy 1 Each heavy atom and its associated hydrogen atoms are rigidly translated. RTRN BYATom 1 Each instance is a displacement of a single atom by a random vector distributed uniformly in an ellipsoid (see the description of the ANISotropic keyword). For historic reasons, the CART keyword is a synonym for RTRN BYATom, but use of the former is discouraged since the moves are not actually based on Cartesiancoordinates. RROT BYALl 1-2 The entire first atom selection specifies the rigid body of atoms to be rotated, and each of the atoms in the second atom selection is an allowed rotation center. The second selection need not be a subset of the first, so rotations around atoms outside the rigid body can occur. If no second atom selection is given (or one is given, but no atoms are selected), the rotations are made around the center of mass of the first atom selection. RROT BYREsidue 1 There is only a single atom selection, and each