CHARMM Element doc/block.doc 1.1#File: BLOCK, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax The commands described in this section are used to partition amolecular system into "blocks" and allow for the use of coefficientsthat scale the interaction energies (and forces) between these blocks.This has a number of applications, and specific commands to carry outfree energy simulations with a component analysis scheme have beenimplemented. The lambda-dynamics, an alternative way of performingfree energy calculations and screening binding molecules, has also beenimplemented. Subcommands related to BLOCK will be described here. To see how to output the results of a dynamics run, please see DYNAMICS documentation (keywords are IUNLDM, NSAVL, and LDTITLE). Please refer to PDETAIL.DOC for detailed description of the lambda dynamics and its implementation. BLOCK was recently modified so that it works with the IMAGEmodule of CHARMM. As some changes to the documentation were necessaryanyways, it was decided to also improve the existing documentation.The Syntax and Function section below are relatively unchanged; theadded documentation is in the Hints section (READ IT if you are usingBLOCK for the first time!). Comments/suggestions [email protected].* Menu:* Syntax:: Syntax of the block commands* Function:: Purpose of each of the commands* Hints:: Some further explanations/hints* Limitations:: Some warnings...#File: BLOCK, Node: Syntax, Up: Top, Next: Function Syntax of BLOCK commandsBLOCk [int]Subcommands:miscellaneous-command-spec ! see *note miscom:(chmdoc/miscom.doc).CALL int atom-selectionLAMBda realCOEFficient int int real - [BOND real] [ANGL real] [DIHEdral real] [ELEC real] [VDW real]NOFOrceFORCeFREE_energy_evaluation [OLDLambda real] [NEWLambda real] - FIRSt int [NUNIT int] [BEGIn int] [STOP int] [SKIP int] - [TEMPerature real] [CONTinuous int] [IHBF int] [INBF int] [IMGF int]INITializeCLEArEnergy_AVeraGe [OLDLambda real] [NEWLambda real] -FIRSt int [NUNIT int] [BEGIn int] [STOP int] [SKIP int] - [CONTinuous int] [IHBF int] [INBF int] [IMGF int]COMPonent_analysis DELL real NDEL int [TEMPerature real] - FIRSt int [NUNIT int] [BEGIn int] [STOP int] [SKIP int] [IHBF int] [INBF int] [IMGF] intAVERage {DISTance int int} {STRUcture} [PERT] [TEMPerature real] [OLDLambda real] [NEWLambda real] - FIRSt int [NUNIT int] [BEGIn int] [STOP int] [SKIP int]LDINitialize int real real real real [real]RMBOnd RMANgleLDMAtrixLDBI intLDBV int int int int real real intLDRStartLDWRite IUNL int NSAVL int RMLAmbda {internal_energy_spec} internal_energy_spec ::== BOND THETa|ANGLe PHI|DIHEd IMPHi|IMPRSAVEUNSAveQLDMQLMC [MCTEmperature real] [FREQ int] [MCSTep int] [MAX real]MCIN int {real .... real}MCDI realMCRSMCLEarLANG [TEMP real]RSTP int realEND#File: BLOCK, Node: Function, Up: Top, Previous: Syntax, Next: Hints 1) BLOCk [int] enters the block facility. The optional integer isonly read when the block structure is initialized (usually the firstcall to block of a run) to specify the number of blocks for spaceallocation. If not specified, the default of three is assumed. 2) END exits the block facility. The assignment of blocks, thecoefficient weighting of the energy function, the force/noforceoption, etc. remain in place. For the terms of the energy functionthat are supported, each call to ENERGY (either directly or throughMINIMIZE, DYNAMICS, etc. commands) results in an energy and forceweighted as specified. The matrix of interaction coefficients isprinted upon exiting. 3) CALL removes the atoms specified by "atom-selection" from theircurrent block and assigns them to the block number specified by theinteger. Initially all atoms are assigned to block 1. If atoms areremoved from any block other than block 1, a warning message isissued. If blocks are assigned such that some energy terms (theta,phi, or imphi) are interactions between more than two blocks, awarning is issued when the END command is encountered. (Take suchwarnings seriously; this is a severe error and indicates thatsomething is wrong. However, the problem might be not the CALLstatement (or the atom selection) itself; quite possibly your hybridmolecule was generated improperly) 4) LAMBda sets the value of lambda to "real". This command is onlyvalid when there are three blocks active. Otherwise multiple COEFcommands may be used to set the interaction coefficients manually. LAMBda x is equivalent to (let y=1.0-x) COEF 1 1 1.0 COEF 1 2 y COEF 1 3 x COEF 2 2 y COEF 2 3 0.0 COEF 3 3 x 5) COEF sets the interaction coefficient between two blocks (representedby the integers) to a value (the real number). When the block facilityis invoked, all of the atoms are initially assigned to block 1 and allinteraction coefficients are set to one. The required real value(first specified) scales all energy terms expect those specific termswhich are named with alternative corresponding scale factors. 6) NOFOrce specifies that in subsequent energy calculations, theforces are not required. This is economical when using thepost-processing commands (FREE,EAVG,COMP). Forces may be turned backon with the FORCe command; this is necessary before runningminimizations and dynamics if there was a prior NOFO command. 7) FREE calculates a free energy change using simple exponentialaveraging, i.e. the "exponential formula". If the old and new lambdas(OLDL,NEWL) are specified (can only be done when three blocks areactive), the perturbation energy is calculated for these values (i.e.FREE gives you the free energy difference between NEWLambda andOLDLambda via perturbation from the lambda value at which yourtrajectory was calculated. If not, the current coefficient matrix isused (FREE should be used with three blocks, and the use of OLDL andNEWL is recommended). FIRSt_unit, NUNIt, BEGIn, STOP, and SKIPspecify the trajectory/ies that is/are to be read (for a furtherdescription see the TRAJ command elsewhere in the CHARMMdocumentation). TEMPerature defaults to 300 K and gives thetemperature value to be used in k_B*T. CONTinuous specifies theinterval for writing cumulative free energies. A negative valuecauses binned (rather than cumulative average) values to be written.Be careful to make sure that you use correct non-bonded lists (see thehints section!) 8)