CHARMM Element doc/rism.doc $Revision: 1.1 $#File: RISM, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax RISM (Reference Interaction Site Model) module ------------------------------------------------ The RISM module allows the user to calculate the site-site radial distribution functions g(r) and pair correlation functions c(r) for a multi-component molecular liquid. These functions can then be used to determine quantities such as the potential of mean force or the cavity interaction term between two solute molecules into a solvent, and the excess chemical potential of solvation of a solute into a solvent. The change in the solvent g(r) upon solvation can be determined and this allows for the decomposition of the excess chemical potential into the energy and entropy of solvation. The code was written as an independent program by Benoit Roux in 1988. Some routines were added and it was adapted for CHARMM by Georgios Archontis in 1992. The help and advice of Hsiang Ai Yu is greatfully ackgnowledged.* Menu* Syntax:: Syntax of the RISM commands* Commands:: Explanation of the commands* Theory:: A brief introduction to the RISM theory* References:: Useful references * Examples:: Input files #File: RISM, Node: Syntax, Up: Top, Next: Commands, Previous: Top Syntax for RISM calculation --------------------------- Invoke of the RISM command in the main charmm input file calls the subroutine RISM() (in rism.src). Once control has been transferred to this subroutine the subsequent commands are interpreted using a parser similar to the CHARMM parser. Main command : RISM [NSTV int] [NSTU int] [NSOL int] Enters the RISM module. NSTV is the keyword to indicate the maximum number of atoms in the solvent molecule (the default is 6 as defined in source/fcm/rism.fcm), must be less than or equal to the default. NSTU is for the maximum number of atoms in the solute molecule(s) (default is 20), must be less than or equal to the default. NSOL is for the maximum number of solutes (default is 2), the allowed values are 1 or 2.STOP leaves the RISM moduleSubcommands:1) Miscellaneous commands ( compare with *note (chmdoc/miscom.doc)Syntax ).GOTO ----LABEl labelname ----OPEN { READ { NAME filename UNIT integer } } ---- { WRITE { NAME filename UNIT integer } } STREam [filename]----- [ UNIT integer]RETUrn ------CLOSe [ UNIT integer ] -----SET { parameter string }---DECR { parameter } { BY value } ----INCR {parameter } { BY value }----FORMat { format-description ((f12.5) or (e12.5) default) }IF { parameter } { EQ } { string } ... command-- { NE } IF { parameter } { GT } { value } ... command-- { GE } { LT } { LE }2) Specific RISM commands------------------------- READ { PARAmeters } [show] [UNIT integer (5)] ---- { STRUcture } { COORdinates {( SOLVENT )} } { { SOLUTE { integer (1) } } } { 2COOr { SOLUTE { integer (1) } } } { ZMATrix {(SOLVENT ) } { {SOLUTE { integer (1) } } }{ 2ZMAtrix { SOLUTE { integer (1) } } } { CS(R) { ( VV ) } { [ UV [ SOLUTE integer (1) ] } { US(R) } { G(R) } { CH(K) [ ( VV ) ] } { DC(R) [ SOLUTE integer (1) ] } { DG(R) }WRITe { TITLe }[ UNIT integer (6)]----- { COORdinates ( SOLVENT ) } { { SOLUTE { (1) integer } } } { CS(R) { ( VV ) } { [ UV [ SOLUTE (1) integer ] } { US(R) } { G(R) } { CH(K) [ ( VV ) ] } { DC(R) [ SOLUTE (1) integer ] } { DG(R) } - [ PLT2 ] [FROM real THRU real] [FORMAT format-spec] { R(I) } { RK(I) }SETUp [ ( LOGFFT ) ] [ NPOINT (512) ] [ DR (0.02) ] [ RMIN (-5.12) ]----- [ FFT ]EDTZm [ ( SOLVENT ) ]----- [ SOLUTE integer (1) ]STATe [ TEMP real (300.0) ] ----- [ DENSITY { segment-name-1 real (0.0) ... segment-name-n real (0.0) } ][ CDIE real (0.0) ]ITERate { VV } \----- { UV } only one of these options{ UU } / ------------------------- / [ (HNC) ] [ PY ] only one of these options ------------------------- [ PY2 ] \ [ XTR { AXTR real (1.0) RXTR1 real (0.0) RXTR2 real (0.0) AXTR(2) real (AXTR(1)) RXTR1(2) real (RXTR1(1)) RXTR2(2) real (RXTR2(1)) ... } ] [ INIT ] [ NCYCLE integer (1) ] [ IUNSCR integer (0) ] [ IUNGR integer (0) ] [ NPRINT integer (NCYCLE) ] [ RMIX real (0.33) ] [ NDMAX integer (25) ] [ TOL real (0.01) [ CDIE2 real (CDIE) ] [ US(R) ] [ G(R) ] [ W(R) ] \ [ TS(R) ] only one of these options [ CAV(R)] [ BD(R) ] / [ SW(1) real (1.0) ] [ SWI(1) real (SW(1)) SWF(1) real (SW(1)) DSW(1) real (0.0) ] [ SW(2) real (1.0)] [ SWI(2) real (SW(2)) SWF(2) real (SW(2)) DSW(2) real (0.0) ] [ SW(3) real (1.0)] [ SWI(3) real (SW(3)) ] [ SWI(3) real (SW(3)) SWF(3) real (SW(3)) DSW(3) real (0.0) ] [ SW(4) real (1.0) ] [ SWI(4) real (SW(4)) ] [ SWI(4) real (SW(4)) SWF(4) real (SW(4)) DSW(4) real (0.0) ]DERIvative [ INIT ] [ SOLU integer (1) ]----- [NCYCLE integer (1) ] [ NPRINT integer (NCYCLE) ] [ RMIX real (0.33) ] [ TOL real (0.01) ] [ CLOS (HNC) ] \ [ PY ] only one of these options [ PY2 ] /SOLVation { HNC } [ CHMPOT ] [ ENER ] [ CAVIT ] [ FLUC ] ----- [ SW(1) ] [ SW(2) ] [ SW(3) ] [ SW(4) ] [ SOLUte integer (1) ] [ VERBO ] [ PLT2 [ FROM real (RMIN) THRU real (RMAX) ] ][ UNIT integer (6) ]ANALysis [ (VV) ]----- [ UV ] [ PAIR integer (all pairs) ] [