CHARMM Element doc/perturb.doc $Revision: 1.3 $#File: Perturb, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax Perturbation: Thermodynamic Perturbation Calculations. * Menu: * Syntax:: Syntax of the set up of the perturbation command.* Description:: Description of the keywords and options for setting up the perturbation calculation. Includes an explanation of the reset command TSM CLEAr.* Post-processing:: How to process the perturbation output of the dynamics run.* Details: (chmdoc/pdetail.doc). How to run perturbation calculations.* Implementation: (chmdoc/pimplem.doc). How it is implemented. Programming details. * CFTI: (chmdoc/cfti.doc). Conformational Energy/Free Energy Calculation (Krzysztof Kuczera)#File: Perturb, Node: Syntax, Up: Top, Next: Description, Previous: Top Syntax for the Perturbation Command [SYNTAX TSM] TSM Chemical Perturbation Parameters:1. REACtant atom_selection_list | NONE 2. PRODuct atom_selection_list | NONE 3. LAMBda <real> [ POWEr <int> ] 4. SLOW TEMP <real> LFROm <real> LTO <real> [ POWEr <int> ] 5. DONT {REACtant} {internal_energy_spec} [SUBTract] {PRODuct} {internal_energy_spec} 6. GLUE {CM FORCe <real> MIN <real>} [SUBR] [SUBP] {ATOMs FORCE <real> MIN <real> atom_spec atom_spec 7. NOKE {REAC} {PROD} 8. SAVE UNIT <integer> [FREQ <integer>] 9. COLO atom_spec PCHArge <real> [RCHArge <real>] atom_spec ::= segid resnum type 10. PIGGyback PIGGy atom_spec BACK atom_spec atom_spec ::= segid resnum type 11. UMBRella 4x( atom_spec) VACTual <real> atom_spec: segid resnum typeInternal Coordinate (IC) Perturbation Parameters:12. FIX {ic-spec} [TOLI <real>]13. MAXI <integer>14. MOVE {ic-spec} 2x{atom-selection} BY <real>15. SAVIc [ICUNit <integer>] [ICFReq <integer>] [NWINdows <integer>]16. END internal_energy_spec ::== BOND THETa|ANGLe PHI|DIHEd IMPHi|IMPRic-spec ::= {[DISTance] 2x{atom-spec} }{[BOND] 2x{atom-spec} } {[ANGLe] 3x{atom-spec} } {[THETa] 3x{atom-spec} } {[DIHEdral] 4x{atom-spec} } {[PHI] 4x{atom-spec} } atom_spec ::= segid resid typeatom-selection ::= see (*Note Select: (SELECT).)----------------------------------------------------------------------- TSM CLEAr Clears heap data structures used in perturbation setup, cancels constraints and perturbations, and resets logical flags.#File: Perturb, Node: Description, Up: Top, Next: Post-processing, Previous: Syntax Explanation of the Perturbation Setup Currently the perturbation setup is initiated by invoking thecommand TSM with nothing else on the command line. This is followed bya number of other commands, listed below, and terminated with an ENDcommand. Two types of thermodynamics perturbations are available: chemi-cal perturbation and internal coordinate perturbation. Each is discussedseparately below.* Menu:* ChemPert:: Chemical Perturbation* ICPert:: Internal Coordinate Perturbation#File: Perturb, Node: ChemPert, Up: Description, Next: ICPert, Previous: Description Chemical Perturbation For chemical perturbations, a minimum of three commands are necessary besides TSM and END: REAC - to specify the reactant atom list; PROD - to specify the product atom list; LAMBda or SLOW to specify lambda for win-dowing or the slow growth technique.1. REACtant atom_selection_list | NONE Specifies the reactant atom list (see *Note details: (pdetail).).The atom selection list uses the standard CHARMM selection command syntax(see *Note Select: (SELECT).). Subsequent invocations of this commandclears the selections of any earlier invocation. 2. PRODuct atom_selection_list | NONE Specifies the product list (see above). 3. LAMBda <real> [ POWEr <int> ] The hybrid Hamiltonian is defined, in this implementation, as H(lambda) = ( (1 - lambda)**N )V(reac) + (lambda**N)V(prod). This command specifies lambda and N. It also indicates that the windowmethod is to be used (see *Note details: (pdetail).). 4. SLOW TEMP <real> LFROm <real> LTO <real> POWEr <int> This command specifies that the "slow growth" (see*Note details: (pdetail).) method be used. LFROm and LTO indicates thelimits of integration. POWEr has the same meaning in the previouscommand. 5. DONT {REACtant} {internal_energy_spec} [SUBTract] {PRODuct} {internal_energy_spec} internal_energy_spec :== BOND THETa|ANGLe PHI|DIHEd IMPHi|IMPR This command indicates that the specified internal energy term(s)for the reactant or product atoms is (are) to be ignored as perturbationinteractions. That means that the specified interactions are notfactored by lambda**N or (1 -lambda)**N and do not contribute to thevalue of V(reac) or V(product). The interaction is, however, computed infull and treated as part of H(env) (see *Note details: (pdetail).). Morethan one internal energy type can be specified at a time but reactant andproduct must be specified in separate commands. The optional sub-commandSUBTract causes specified perturbation forces on the environment atoms(see *Note details: (pdetail).) to be subtracted. This is verynon-Newtonian and was included as an early (and largely unsuccessful)attempt to generate configurations at lambda = 0 and 1 for thenon-existent group. See the discussion of the endpoint problem, (in*Note details: (pdetail).), also known as the lambda goes to zerocatastrophe (Beveridge, 1987). Anyway, what this does is remove theforces due to terms specified in the DONT option from the environmentatoms involved. In addition, the terms are not lambda factored orincluded in H(lambda) or in V(reac) or V(pert). The forces are left onthe perturbed atoms with the hope that this would produce usableconfigurations. It does not. Rather, the atoms drag along and badnon-bond contacts result when lambda is 0 or 1 (the original intendeduse). We generally use the DONT option for both reactant and productfor the bond stretching and bending terms. These terms are generallyuncoupled from the interactions of interest and it