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

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 module Subcommands: 1) Miscellaneous commands ( compare with *note (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) ] [ UNIT integer (6) ] STOP ---

Explanation of the RISM-specific commands ----------------------------------------- 1. Miscellaneous commads ------------------------ These commands are similar to the ones recognised by the miscom.src routine (see note* (miscom.doc)Syntax ). We will only mention the following differences: a) The command OPEN should not contain the keyword CARD or FILE; all files are opened FORMATTED b) The command CLOSe should not be followed by a DESPosition statement; all files are closed with DESPosition KEEP. c) The command FORMat defines the format of the internal parameters and should be of the form (format-specification) and up to 7 characters long (e.g. (f12.6). 2. RISM-specific commands ------------------------- The READ command ------------------ READ PARAmeters [ show ] [ UNIT integer (5) ] In the beginning of a RISM calculation the parameters for the various atoms should be specified. The option show will print into the output file the parameters for all possible atom pairs. For all READ options one can explicitly specify an input file from where the information will be read. If a [UNIT integer] option is not given, the default (5) is assumed. The format for parameter input is: READ PARAMeters * title * [COMBIne {(STANDARD)} ] { JORGE } NBOND atom-name epsilon rmin/2 charge (free format) ..................................... END ! of NBOND NBFIX atom-name epsilon rmin (free format) END ! of NBFIX END ! of PARAMETERS The option COMBINE STANDARD (default) uses the addition rule for sigma's whereas JORGE uses the multiplication rule. The epsilon value is the well depth; It can be specified positive or negative since the code converts it to its absolute value. ================================================================== READ STRUcture [ show ] [ UNIT integer (5) ] This command reads the information about the atoms in the solvent and solute molecules and the type of sites. Two sites are labeled with the same integer only when they have the same vdw parameters and charge AND they are geometrically equivalent. For example, in tip3p H2O the sites for the 2 hydrogens are equivalent because they are symetrically placed with respect to oxygen. (NOTE that if two sites are geometrically equivalent but are given different site index this will not affect the calculation; the opposite will lead in erroneous results). The format of the structural input is: READ STRUCTURE [show] *title * SOLVENT NSITE integer (0) NTYPE integer atom-1 atom-name TYPE integer [SEGID name] [RESNAm name] [coordinates] ..................................................................... [ZMATRIX] atom atom atom bondlength atom atom bondlength atom theta atom atom bondlength atom theta atom phi SOLUTE 1 NSITE integer (0) NTYPE integer atom-1 atom-name TYPE integer [SEGID name] [RESNAm name] [coordinates] ..................................................................... [ZMATRIX] ..................................................................... SOLUTE 2 NSITE integer (0) NTYPE integer atom-1 atom-name TYPE integer [SEGID name] [RESNAm name] [coordinates] ..................................................................... [ZMATRIX] ..................................................................... END ! of structure The parameter NSITE should be equal to the number of atoms in the molecule. If no specification is given the default value NSITE=0 is assumed. NTYPE should equal the number of different sites. If NTYPE is not specified explicitly the default value NTYPE=NSITE is assumed. After the line NSITE...NTYPE the various atoms are defined. atom-1 is the (user given) name for the first atom, atom-name is the name of this atom in the parameter list. TYPE is followed by the type of the atom. The keywords SEGID and RESNAm specify the segment id and the name of the residue to which the atom belongs. If the keywords SEGID and RESNAm are not mentioned, the names SOLV, SOLU1,SOLU2 are assumed for the solvent and the two solutes. If they are mentioned, all atoms in the following lines are assigned to the same SEGID and RESNAm until a line with a new explicit specification is encountered. Notice that atoms that have different SEGID belong to different molecules. This has the implication that the w matrix element for those sites will be set to zero. This is useful when one wants to define a pure solvent mixture of many components. The atom-definition line can contain the coordinates for this atom.The coordinate specification is important only because it allows the program to calculate the distances between the various atoms in the structure and construct the intramolecular matrix w. Since the integral equation technique involves an average over all space, the coordinates of the solvent/solute(s) and their relative location in space (which is important in MD/MC simulations) here does not have any other significance. Alternatively, one can append after the atom-definition lines the ZMATRIX description of the molecule and avoid explicit reference to the atomic coordinates. ===================================================================== READ COORdinates ( SOLVENT ) [ UNIT integer (5) ] { SOLUTE { (1) integer } } This command allows the program to read the coordinates from an input file in CHARMM format. The meaning of coordinates in RISM was explained a few lines before. ====================================================================== READ 2COOr SOLUTE { 1 } integer } [UNIT integer (5) ] This command allows the program to read the coordinates for a second structure in CHARMM format. This second set of coordinates is used in calculating the change in chemical potential due to a conformational transition of the solute from the structure 1 (read by READ COOR) into the structure 2. Note that the keyword SOLUTE must be appended after 2COOR, otherwise the second set of coordinates will be given to the solvent. (see also *note (rism.doc)Theory, section 5 ). ===================================================================== READ ZMATrix ( SOLVENT ) [ UNIT integer (5) ] { SOLUTE { (1) integer } } This command reads explicitly the ZMATRIX. The format is: READ ZMATRIX SOLVENT * title * atom atom atom bondlength atom atom bondlength atom theta atom atom bondlength atom theta atom phi ===================================================================== READ 2ZMAtrix { SOLUTE { (1) integer } } [ UNIT integer (5) ] This command reads the ZMATRIX for the second structure of the solute. This structure is used in calculating the change in chemical potential due to a conformational transition of the solute from structure 1 (generated after the command READ...ZMAT was issued) to structure 2. (see also *note (rism.doc)Theory, section 5 ). ====================================================================== READ { CS(R) { ( VV ) } [UNIT integer] { [ UV [ SOLUTE (1) integer ] } { [ UU [ SOLUTE integer (1) ] [ SOLUTE integer (1) ] } { US(R) } { G(R) } This command reads the short ranged direct correlation function cs(r), (see *note (rism.doc)Theory, section 2) the short range potential us(r) (usually van der waals or whatever the user wants to define as short-ranged, provided that it can be fourier transformed) or the radial distribution function g(r). The short-ranged potential us(r) should not contain the coulombic interaction between the sites, since this is added separately (see *note (rism.doc)Theory, section 2)). The various distribution functions are stored as arrays (dvect X npair). The left index labels the point in r or k-space and the right index labels the pair. For example, the vv csr(4,1) stores the function for the vv pair 1 at the 4th point of the discrete representation of space. The format of the files where the distribution functions are stored is the following: * Title * NPOINT, N-DISCRETE-PAIR SW(1) SW(2) SW(3) SW(4) A(1,1) A(2,1) A(3,1) ... A(NPOINT,1) A(1,2) A(2,2) A(3,2) ... A(NPOINT,2) ..................................... The keywords VV,UV,UU define whether the input functions refer to the solvent-solvent, solute-solvent or solute-solute pairs respectively. If the selection is not specified the solvent (VV) is asumed as a default. The keyword SOLUTE specifies which solute the uv and uu functions should be attributed to. Note that the default is SOLUTE 1 (e.g. the command READ CS(R) UU UNIT 10) will read from unit 10 the cs(r) and consider it as the solute 1 solute 1 function. ===================================================================== READ CH(K) [ ( VV ) ] [ UNIT integer ] This reads the solvent-solvent susceptibility in fourier space. The vv susceptibility is defined as ch(v,v',k) = w(v,v',k) + rho(v) h(v,v',k) rho(v') (for an explanation of these symbols see *note (rism.doc)Theory, section 1). ===================================================================== READ { DC(R) [ SOLUTE (1) integer ] } [UNIT integer] { DG(R) } Read the derivative of the solvent-solvent direct correlation or radial distribution function with respect to the solute density. The keyword SOLUTE specifies which solute causes the solvent responce. (for an explanation of these functions see *note (rism.doc)Theory, section 4). ===================================================================== The WRITe command The WRITE command is similar with the READ command. The only additional keywords associated with the command WRITE..X (X == distribution function) are : [PLT2] [FROM real THRU real ] [FORMAT format-spec] that asks the program to print the data in columns and as a function of the r (or k) coordinate. FROM declares the starting point for the printing and THRU declares the last point (defaults are the first and last point). The FORMAT is followed by a format specification (character*80) (default is (1X,25F10.3) ). This is different than the FORMAT command, that defines the format of the internal parameters. WRITE R(I) [UNIT integer] RK(I) will print the points in r- or k-space respectively. (see *notes (rism.doc)Theory, Section 2). ===================================================================== The SETUp command SETUp { ( LOGFFT ) } [ NPOINT (512) ] [ DR (0.02) ] [ RMIN (-5.12) ] { FFT } This command initializes the variables related to the fast fourier transform that is a part of the iteration cycle (see *note (rism.doc)Theory, Sections 2, 3 ). The FFT on a logarithmic scale is the default. If the keyword FFT is specified a FFT on a linear scale will be performed (the logfft works better). KEYWORD FUNCTION LOGFFT The FFT on a logarithmic scale will be performed (in the CONVEX the program uses the veclib routine). LOGFFT is the default. FFT Use a linear scale FFT. NPOINT The number of points to be used in the FT (POWER OF 2) The default is 512 which gives convergent results for most applications with the LOGFFT. Before increasing the number of points used, one should first redefine the maximum number of points used (DVECT) that is stored in rism.fcm and is currently set to DVECT=512. DR The spacing in r or k space RMIN The minimum value used for the log-scale r and k-space variables (see note* (rism.doc)Theory, Section 2). ===================================================================== The EDTZm command EDTZm [ ( SOLVENT ) ] [ SOLUTE integer (1) ] This command edits the ZMATRIX for the solvent or solute. The format for the command is: EDTZm SOLVENT ENTR integer BOND real THETA real PHI real .................................................. END The ENTR specifies the # of line of the original ZMATRIX that is to be modified. ===================================================================== The STATe command STATe [ TEMP real (300.0) ] [ DENSITY { segment-name-1 real (0.0) ... segment-name-n real (0.0) } ] [CDIE real (0.0)] This command allows the input of various thermodynamically important variables. The meaning of the various keywords is: KEYWORD FUNCTION TEMP defines the temperature of the solution. DENSITY defines the density of the various solvent segments. (this is the numerical density, #of sites/A**3). Each site in RISM is associated with a density (see *note (rism.doc)Theory, Section 1). Each segment-name has been defined in the READ STRUcture command and defines a distinct solvent molecule (in the usual case of the one-component solvent one needs to define one solvent segment only). Therefore, all sites that belong to this segment will be assigned the same density. If there are additional solvent segments and they are not explicitly mentioned their density will be set to zero. CDIE defines the macroscopic dielectric constant of the solution. This macroscopic information is needed to correct for the asymptotic behavior of the direct correlation functions c(r). (see *note (rism.doc)Theory, Sections 2, 3). If CDIE is followed by a negative number the natural dielectric constant is simply printed in the output, but no adjustement of the charges is done. If CDIE is positive the coulombic charges are adjusted so that the long range properties of c(r) are consistent with the CDIE given. If the keyword CDIE is omitted no action is taken. NOTE that because the correction assumes neutral molecules, the CDIE should not be specified for salt solutions. ===================================================================== The ITERate command This is the command that starts the iteration cycle that solves the RISM integral equations (see *note (rism.doc)Theory Sections 1 and 2). Invoke of the command ITERate transfers control to the subroutine cycles (cycles.src), which parses the command line and calls the appropriate routines. All keywords that follow the word ITERate should be included in the same line (lines are appended if they end with a hyphen, as usual). The keywords used are: KEYWORD FUNCTION VV Define whether the iteration cycle will solve the UV solvent-solvent (VV) , solute-solvent (UV) or solute- UU solute equation. HNC Define the type of closure used (HNC is the default). PY (see *note (rism.doc)Theory Section 1) PY2 Currently the XTR closure is implemented only for the XTR pure solvent calculation. When use XTR one should read first the vv g(r), since this closure uses g(r) and solves for the so called bridge function and the direct corellation function cs(r). INIT This keyword signifies that the cycle is initialized. NCYCLE The maximum number of cycles to be executed. NPRINT The frequency of printing out the change in the direct correlation function cs(r) TOL The tolerance that has to be satisfied in order for the iteration loop to stop (if icycle < NCYCLE). At each iteration step the maximum change in the function csr (dmax) is determined and compared with the tolerance. If dmax < tol the loop exits. RMIX The mixing coefficient between the most recent cs(r) and the cs(r) of the previous cycle. (see *note (rism.doc)Theory Section 2). If the iteration overflows one should generally restart the computation with larger rmix. NDMAX The frequency of checking the dmax. In principle, the iterations should converge by achieving gradually reduced dmax. If the iterations start to diverge the dmax will increase with each cycle. Every NDMAX steps the program compares DMAX with the value stored in the previous check. If the new dmax is found larger than before, the coefficient RMIX is increased. IUNCSR The unit number of the files to which cs(r) and g(r) are IUNGR to be stored after the calculation. These keywords can be omitted and the functions can be written to files using explicit WRITE statements, after the iteration loop has been completed. CDIE2 Keyword that can be used in the UU calculation to determine the diel. constant modifying the molecule- molecule coulomb energy. The default CDIE value, defined in the command STATE is otherwise used. US(R) Determines that the short range interaction that has been read from an input file should be used. In this case the van der Waals parameters specified in the parameter list are not used. This is useful if one wants to use a more general short range potential. This option can also be used if one wants to reconstruct the g(r) after having determined the bridge function via the XTR closure. NOTE that the input file should contain the potential us(r)/KT. G(R) Determines that the g(r) should be constructed. This keyword is not needed in the other closures expect XTR, since for all other cases the g(r) is automatically constructed. W(R) Store the potential of mean force in the auxiliary array us(r). This can be subsequently written into a file with the WRITE US(R)... statement. TS(R) Store the function h-c in the auxiliary array us(r). BD(R) Store the function us(r)/KT-bridge in the auxiliary array us(r). If this function is read before a vv calculation and the keywords US(R) and HNC are used, the function g(r) (that produced the bridge) can be reconstituted. (see *note (rism.doc)Theory, section 1). CAV(R) Store the cavity term -KT*(h-c+coulomb/(cdie*KT)) in the auxiliary array us(r). This keyword is used in the UU calculation only. The coulomb term describes the coulomb interaction between the solute MOLECULES and is divided by the dielectric constant cdie (that is equal to the macroscopic dielectric defined in the command STATE). For monoatomic solutes the term cav is equal to the solvent-mediated interaction that the two solutes would have if their direct coulombic interaction were equal to coulomb/cdie. Thus, this cavity term can be added to the CHARMM intramolecular energy for which a cdie value has been used, to reproduce the total vacuum + solvent-mediated molecular energy (see also ref. [10] ). SWI(n) The iteration loop can be executed inside a switching SWF(n) loop that gradually switches on the interactions. This DSW(n) prevents from numerical divergence. The integer n defines the kind of switch used: SW(n) n=1 - scale the total energy n=2 - scale the sigma n=3 - scale the coulombic charges n=4 - scale the bridge function (used in VV only in conjuction with the XTR closure. SWI() defines the beginning value of the switching coefficient, SWF() defines the final value and DSW() the step used. One can simply specify the switching coefficients by SW() and perform the iteration for the particular value of SW() (without looping over the switch). AXTR The following 6 keywords describe switching parameters RXTR1 associated with the XTR closure and the bridge calculation RXTR2 The switch in this case is performed with a shifting AXTR(n) function. AXTR describes the maximum value of the RXTR1(n) shifting function, RXTR1 the point in r-space (in A) RXTR2(n) where the shifting function starts diminishing and RXTR2 the point where it vanishes. If the first three keywords are used then the same values are assume for all pairs. The explicit appearance of one of the last keywords defines the value for the respective switch of pair n. ===================================================================== The DERIvative command This command starts the iteration cycle that calculates the derivatives of the solvent-solvent g(r) and cs(r) with respect to the solute density (see *note (rism.doc)Theory, Section 4 and ref. [1]. The syntax of the command is similar to the ITERate command. Below we explain only the keywords that differ from the ones in the ITERate command. KEYWORD FUNCTION INIT Used in the beginning of the cycle to zero the dcs(r). SOLU defines the solute, the responce to which we calculate. (Remember that dcs(r) and dg(r) refer to solvent-solvent quantities). ====================================================================== The SOLVation command This command calculates the excess chemical potential of solvation (see *note (rism.doc)Theory, Section 4 and [2]). The keywords are: KEYWORD FUNCTION CHMPOT Calculate the chemical potential using the closed form for the HNC-derived huv and cuv. ENER Calculate the solute-solvent interaction energy. This is a part of the total energy of solvation. CAVITy Calculate the solvent reorganization energy. In order that this term be calculated the solvent responce dg(r) and dcs(r) must have been found first. FLUC Find the change in the chemical potential upon a conformational transition of the solute (see *note (rism.doc)Theory, Section 5). HNC The closure used. This should be consistent with the closure used in calculating the g(r) and cs(r). Currently only the HNC closure is implemented for the SOLVation calculation. SW(i), i=1,..4 Describes the switch to which the the distribution functions used in the calculation correspond. The default is SW(n)=1. VERBO Decompose the chemical potential and the interaction energy into the contribution of the individual solute-solvent site pairs. If the FLUC keyword exists, then VERBO decomposes the change in chemical potential to the contributions of the INTRAMOLECULAR site pair terms. PLT2 Plots the integrands in real space of the expression FROM for the chemical potential and the interaction THRU energy. Thus, one can get a feeling about which terms contribute and at what distances. UNIT Defines if another output unit than the standard should be used. ===================================================================== The ANALysis command This command prints the locations of the first three maxima and minima for the g(r) and the coordination numbers. KEYWORD FUNCTION VV Defines whether the vv or uv g(r) is to be printed UV PAIR Defines if a particular pair is to be printed (default=all pairs). UNIT Defines if another output unit than the standard should be used. =====================================================================

A brief introduction to the RISM theory --------------------------------------- 1. The RISM equations --------------------- A basic concept in the statistical mechanical theory of dense systems is the radial distribution function g(r). This function provides information about the local structure of a liquid, because it gives the number of atoms that exist in a sphere of radius r around any other atom via the relation: N(r) = 4 pi r**2 rho g(r) dr (1) where rho is the bulk density of the system. Using g(r) one can calculate other useful quantities, such as the average interaction energy between a solute atom and the solvent ENER = 4 pi Integral{ r**2 rho g(r) Uuv(r) dr } (2) where Uuv(r) is the direct interaction between the solute and the solvent atoms at a distance r, or the excess chemical potential dUuv(lambda) chem. pot. = Integral { < ------- > dlambda }(3) dlambda lambda The radial distribution function has been assumed to depend only on the distance r that separates two atoms. This is true for isotropic atomic liquids, but the situation becomes more complicated for the case of molecular liquids. In this case the interaction between two molecules depends on their relative orientation. Therefore, the molecular liquid radial distribution function will depend in general not only on the distance r but also on the solid angles that define the orientation of the molecules. The RISM integral equation theory [3-6] assumes that molecules can be decomposed into atomic sites. A molecular mixture can thus be viewed as a mixture of atomic sites. Each site is surrounded by sites of two kinds: 1) the ones that belong to the same molecule and 2) the ones that belong to different molecules. Sites of the same molecule are constrained to be at specific distances from each other (i.e. the molecules are assumed to be rigid). The objective then is to determine the g(r) between sites that belong to different molecules. Since each site carries along a whole bunch of sites that are rigidly separated from it, the (intermolecular pair) g(r) will depend not only on the particular pair of sites but also on the other sites of the two molecules. The RISM integral equation is a matrix equation of the form: ------ rho h rho = rho w*c*w rho + rho w*c*rho h rho (4) with rho(i) the array of atomic sites, h(i,j)=g(i,j)-1 and c(i,j) the direct correlation function between sites i and j. The star * denotes convolution. Eq. (4) is reminiscent of the atomic Ornstein- Zernike equation and it can be considered as the defining equation for c. Since it is a convolution equation, it acquires a very simple form upon fourier transformation, becoming a product of matricies. The matrix w has elements in Fourier space: w(i,j) = 0 i,j in different molecules sin(k Lij) (5) ---------- i,j in the same molecule Lij Thus, in r space the matrix w(i,j) is a delta function which constrains the sites i and j to be at a distance Lij. Sites that belong to different molecules decouple, as (5) indicates. The array rho runs through all atomic sites of the molecular mixture. Obviously, all atomic sites that belong to the same molecular species have the same density (equal to the density of the species). Equation (4) can be simplified considerably if (at least) one molecular species (and thus all atomic sites associated with it is considered to have zero density (this is called the limit of infinite dilution). This assumption is made for the case of solute-solvent and solute-solute calculations, where the solute species is assumed to have zero density. Thus, equation (4) can appear in one of three different forms (v denotes solVent and u denotes solUte sites): 1) solvent-solvent ------------------ The solvent density is not zero. Dividing (4) by rho(v)*rho(v') one gets: h(v,v') = w(v,v')*c(v',v'')*w(v'',v) + w(v,v')*c(v',v'')*rho(v'')h(v'',v) (6a) 2) solute-solvent ----------------- in this case the density of the solute sites rho(u)=0. The resulting equation is: h(u,v) = w(u,u')*c(u',v')*w(v',v) + w(u,u')*c(u',v')*rho(v')h(v',v) (6b) The assumption rho(u)=0 prevents the intermolecular coupling of solute-solute sites that would lead to an additional term w(u,u')*c(u',u'')*rho(u'')h(u'',v) (7) Thus, equation (6b) contains only the solvent-solvent distribution function h(v',v) in the r.h.s., that can be calculated separately in the solvent-solvent calculation. 3) solute-solute ---------------- again the solute density rho(u)=0. The solute-solute equation is: h(u,u') = w(u,u'')*c(u'',u''')*w(u''',u') + w(u,u'')*c(u'',v)*rho(v)h(v,u') (6c) As before, in the zero density limit the r.h.s contains only the solute - solvent distribution function that can be solved separately with equation (6b). Equations (6a-6c) contain two unknown functions: the radial distribution function h=g-1 and the direct correlation function c. In order to solve them one uses a second equation (closure) that completes the system of equations. The closures used in RISM are inspired by the statistical mechanical theory of the atomic liquids, where a diagrammatic analysis provides with an exact equation between h,c and the so called "bridge function" b [3], to which equation the various closures are approximations. The exact atomic equation is given by: h = exp { -u/KT +h -c +b } -1 (8) The bridge function is unknown and thus (8) cannot be used in its exact form. The simplest approximation is to set b=0 and get the so called HNC closure (works better for long range interactions). In RISM one makes the assumption that the h(a,b) between the atomic sites a and b satisfies a closure equation identical to the atomic case equation (8) and then one approximates (8) with one of the following forms: ---------------------------------------------------------------------- CLOSURE EQUATION HNC : h(a,b) = exp { -u(a,b)/KT +h(a,b) -c(a,b) } -1 (9a) PY : h(a,b) = exp { -u(a,b)/KT } (1 +h(a,b) -c(a,b) ) -1 (9b) PY2 : h(a,b) = exp { -u(a,b)/KT } X (1 +h(a,b) -c(a,b) + 0.5 (h(a,b)-c(a,b))**2 ) (9c) with a, b solvent and/or solute sites. ---------------------------------------------------------------------- Thus, the approximation made in adopting one of the above closures with RISM is twofold: a) one extends the atomic case equation (8) to RISM and b) one approximates further by simplifying (8). The approximations involved and the uncertainty in the parameters used for the potential u(a,b) result in a calculated g(r) that does not match exactly the experimental (or MD/MC) calculated g(r). One can follow an alternative route and use the g(r) that results from experiment or simulations as an input in equations (6) and (8) to determine the functions h and b. This is referred to as the XTR closure in the RISM module. The function -b can then be added to the short-range potential and the initial g(r) can be reconstructed using the effective potential u-KT*b and the HNC closure. This is similar to the Reference HNC or RHNC method explained in [3]. 2. Description of the iteration method -------------------------------------- In order to calculate the g(r) of a molecular mixture one defines first the solvent and the solute (if there is any) molecular species. The solvent-solvent equation (6a) along with one of eqs (9) is solved first. The direct correlation function c(v,v') tends asymptotically (at large distances) to the form: c(v,v') --> -coulomb(v,v')/KT (10) as can be easily seen from (9). Since the solution of (6) involves fourier transformations and the coulomb potential 1/r decreases very slowly with distance, one separates c(v,v') in a short ranged part cs(v,v') and a long ranged part as follows: c(v,v') = cs(v,v') + coulomb(v,v')/KT (11) Using this separation, the HNC (for example) closure becomes: h(a,b) = exp { -u*(a,b)/KT +h(a,b) -cs(a,b) } -1 (9a') with u*(a,b) the short ranged (van der Waals) interaction between a and b. Denoting as ts the function ts = h-cs, one can write (9a') as cs(a,b) = exp { -u*(a,b)/KT +ts(a,b) } -ts(a,b) -1 (9a'') One can also express (6a) in terms of ts and cs. Then, one starts with the inital guess cs(r)=0 and calculates the fourier transform of (6a) to get ts(k). Taking the inverse F.T of ts(k) and plugging into (9a'') one gets a new guess for csr. Then one F.T. cs(r), substitutes into (6a) and repeats the iteration cycle until the function cs(r) does not change more than a specified tolerance. To decrease the numerical instability one mixes the cs(r) of the most recent cycle (i) with the one of the previous cycle (i-1) according to the prescription csr = (1-rmix) csr + rmix csr (12) i i i-1 After the solvent-solvent h(v,v') has been calculated, one can follow the same iteration procedure to calculate the solute-solvent h(u,v) from (6b). Subsequently, use of h(u,v) and equation (6c) gives the solute-solute h(u,u'). The fast fourier transformation can be performed in a linear scale, where the r-space grid is uniformly spaced, or in a logarithmic scale (this is the default). In the latter case the grid points are defined by the equation: r(i) = exp { -rmin + dr (i-1) } (13) For a description of the algorithm see [7]. The advantadge of the log fft is that the grid is more dense at small distances, where the distribution functions vary more rapidly. The default values used are rmin=-5.12 and dr=0.02 giving r(1)=0.00598 and r(512)=164.02191 for 512 grid points. The log fft with these defaults has been found to give convergent results for most of the cases. 3. Long range behavior of the RISM correlation functions -------------------------------------------------------- As was mentioned in the previous section, the closure equations force the site-site c(r) to decay following a coulomb law (for charged sites). This leads to erroneous estimations of long range properties, such as the dielectric constant. It has been shown [8] that a simple modification of the asymptotic form for c(r) restores the consistency with the macroscopically observed dielectric constant. The modification is achieved by multiplying the coulombic charges of the sites with a constant A that is site independent and is given by the equation 1 + cdie ( 3 y -1) A = ------------------ (14) 3 y (cdie -1) where y is given by 4 pi rho(v) y = ----------- (dipole**2) (15) 9 KT and dipole denotes the dipole moment of the solvent (see also [9]). 4. Chemical potential --------------------- After determining the solute-solvent g(r) one can calculate the excess chemical potential of solvation using eq. (3). The advantadge of using the HNC closure is that it provides a closed form for the chemical potential (see ref. [2] ) : chem. pot. = KT SUM rho(v) [ 0.5 Integral { huv**2 dV } u,v -0.5 Integral { huv cuv dV } - Integral { cuv dV } ] (16) The chemical potential can be decomposed into the energy and entropy of solvation. The energy of solvation is a sum of two parts: a) the solute-solvent interaction energy: ----------------------------------------- interaction energy = SUM rho(v) [ Integral { guv Uuv dV } ] (17) u,v b) the cavity reorganization energy: ------------------------------------ cavity energy = SUM 0.5 rho(v)**2 [ Integral { dgvv' Uvv' dV } ](18) v,v' In (18) with dgvv' we denote the (of order O(rho(u))) change in the solvent-solvent density. More specifically, the solvent-solvent g(r) depends on the solute density. If one expresses the dependence as a power series in the solute density: g(v,v') = g(v,v',lambda=0) + dg(v,v') rho(u) + ... (19) then the function dgvv' of (18) is the second term of (19). With g(v,v',lambda=0) we denoted in (19) the solvent-solvent g(r) without the solute present. Since g(v,v') depends on rho(u) the solvent-solvent energy will be slightly modified upon solvation, contributing to the energy of solvation. As has been shown in [1], the cavity energy persists even in the limit of infinite dilution, but it does not contribute to the chemical potential because it is cancelled exactly by a term in the entropy of solvation. In order to use (18) one must of course determine the function dgvv. This is accomplished by solving a set of equations which result from (6) and (9) upon variation with respect to density. To compare the resulting dgvv with the undisturbed solvent gvv it is useful to multiply dgvv by rho(v) (as suggested by (18)). 5. Dependence of the chemical potential on the solute structure. ---------------------------------------------------------------- As was mentioned in section 1, RISM assumes that the molecules under consideration are rigid. Upon a change in the molecular structure the environment around a particular pair of sites changes, modifying thus the resulting h and c functions. This is mathematically expressed by the fact that the matrix w appearing in (6) will change. In principle, if one is interested to explore the dependence of the solvation chemical potential on the solute geometry, one needs to perform a full calculation for each solute structure. For solutes with many degrees of freedom an exhaustive search of the conformational space can be very time consuming. To avoid this, one can start with eqs. (6b) and (9a) and deduce variational expressions for h, c and the matrix w. Then, one can use the closed HNC expression for the chemical potential to calculate the change in chemical potential upon a conformational change from structure 1 to structure 2 as follows: chmpot(2) - chmpot(1) = - 0.5 KT SUM Integral { c(u,v,1) x(v,v') u,u' c(v',u',1) (w(u,u',2)-w(u,u',1)) } (20) As (20) indicates, one needs to perform a full RISM calculation only once and determine the function c(u,v,1) that corresponds to a particular structure 1. Then, to estimate the potential of any structure 2 one only needs to supply (20) with the new coordinates. Note that (20) is a sum over intramolecular site pairs, in contrast to the expression for the chemical potential. Each term of the sum gives the contribution to the change in chemical potential of the corresponding pair of sites in the structure. By comparing these terms one can conclude which parts of the structure are mostly responsible for the change in chemical potential.

References ---------- [1] H. A. Yu, and M. Karplus, JCP (1988) 89, 2366-2379. A thermodynamic analysis of solvation. [2] S.J. Singer and D. Chandler, Mol. Phys. (1985), 55, 621-625. Free energy functions in the extended RISM approximation. [3] J. P. Hansen and I. R. Mcdonald, Theory of Simple Liquids, 2nd Edition, Academic Press, (1986). [4] D. Chandler, The liquid state of matter: Fluids, simple and complex. E.W. Montroll and J.L. Lebowitz (editors), North Holland Publishing Company, 1982, 275-340. [5] F. Hirata and P.J. Rossky, Chem. Phys. Lett. (1981) 83, 329-334. An extended RISM equation for molecular polar fluids. [6] F. Hirata, P.J. Rossky and M. B. Pettitt, JCP (1983), 78, 4133-4144. The interionic potential of mean force in a molecular polar solvent from an extended RISM equation. [7] P. J. Rossky and H. L. Freedman, JCP (1980), 72, 5694. Accurate solutions to integral equations describing weakly screened ionic systems. [8] P. J. Rossky, M. B. Pettitt and G. Stell, Mol. Phys. (1983), 50, 1263-1267. The coupling of long and short range correlations in ISM liquids. [9] D. Chandler, JCP (1977), 67, 1113-1124. The dielectric constant and related equilibrium properties of molecular fluids: Interaction site cluster theory analysis. [10] M. B. Pettitt, M. Karplus and P. J. Rossky, JPC (1986), 90, 6335-6345. Integral equation model for aqueous solvation of polyatomic solutes: Application to the determination of the free energy surface for the internal motion of biomolecules. [11] H. A. Yu, B. Roux and M. Karplus, JCP (1990) 92, 5020-5033. Solvation thermodynamics: An approach from analytic temperature derivatives.

Input files : 1) vv calculation 2) uv uu derivative --------------------------------------------------------------------- FIRST INPUT FILE --------------------------------------------------------------------- * CHARMM input file for the RISM calculations * test the pure solvent calculation * use tip3p water as solvent * ! enter the RISM module RISM ! read the parameters read parameters show * PARAMETERS for RISM (from CHARMM) * NBOND ! Solvent: ! epsilon Rmin/2 Charge ! epsilon needs not be given as negative ! OT 0.1591 1.60000 -0.834 HT 0.0498 0.80000 0.417 NH1 0.23840 1.60000 -0.350 ! NH1 H 0.04980 0.80000 0.250 ! H CH1E 0.04860 2.36500 0.100 ! CH1E CH31 0.18110 2.16500 0.100 ! CH3E C -0.12000 2.10000 0.550 ! C O -0.15910 1.60000 -0.550 ! O CH32 -0.18110 2.16500 -0.100 ! CH3E CH4 -0.294 2.09300 0.00 END ! the list of specific solute-solvent pairs: NBFIX !Solvent molecule ! epsilon Rmin ! OT OT -0.15207 3.53650 HT OT -0.08363 1.99270 HT HT -0.04598 0.44900 END ! (of NBFIX) END ! (of parameters) ! now read the strucutre read structure show * structure for the solvent * ! read the type of solvent sites solvent nsite 3 ntype 2 OT OT type 1 segid BULK resnam TIP3 HT1 HT type 2 HT2 HT type 2 ! and its geometry via a ZMATRIX ZMATRIX OT HT1 OT 0.9572 HT2 OT 0.9572 HT1 104.52 END ! define the temperature, the density and the macroscopic dielectric ! constant state temp 298.15 density BULK 0.03334 cdie 78.6 ! start the iteration cycle to calculate the vv cs(r) and g(r) iterate vv hnc ncycle 500 nprint 1 - init swi(1) 0.01 swf(1) 0.10 dsw(1) 0.01 - tol 0.9 rmix 0.39 iterate vv hnc ncycle 500 nprint 1 - swi(1) 0.1 swf(1) 1.0 dsw(1) 0.1 - tol 0.9 rmix 0.39 iterate vv hnc ncycle 5000 nprint 10 - tol 0.00001 rmix 0.39 ! print out the characteristics of g(r) for pair 1 analysis vv pair 1 ! now for all pairs analysis vv ! write the calculated distribution functions ! first cs(r) open write name tip3p-charmm.csr unit 20 write cs(r) vv unit 20 * cs(r) for tip3p calculated with the charmm executable * close unit 20 ! then g(r) open write name tip3p-charmm.gr unit 20 write g(r) vv unit 20 * g(r) for tip3p water with the charmm-prepared executable * close unit 20 ! write the g(r) in formmatted form as a function of distance open write name tip3p-charmm-plt2.gr unit 20 write g(r) vv plt2 all from 0.5 thru 10.0 format(1x,10f10.5) unit 20 * g(r) for water with the charmm-prepared executable * r(i) O-O O-H H-H * close unit 20 ! exit RISM stop ! exit CHARMM stop !--------------------------------------------------------------------- SECOND INPUT FILE ---------------------------------------------------------------------- * input test file for the uv calculation * the uu calculation * the derivative calculation * ! enter the RISM module RISM NSTV 3 NSTU 2 NSOL 2 ! test the solute-solvent cs(r) and g(r) calculation ! use tip3p water as solvent ! read first the parameters; show will produce a detailed output ! read parameters show * PARAMETERS for RISM (from CHARMM) * NBOND ! Solvent: ! epsilon Rmin/2 charge ! OT -0.1591 1.60000 -0.834 HT -0.0498 0.80000 0.417 NH1 -0.23840 1.60000 -0.350 ! NH1 H -0.04980 0.80000 0.250 ! H CH1E -0.04860 2.36500 0.100 ! CH1E CH31 -0.18110 2.16500 0.100 ! CH3E C -0.12000 2.10000 0.550 ! C O -0.15910 1.60000 -0.550 ! O CH32 -0.18110 2.16500 -0.100 ! CH3E CH4 -0.294 2.09300 0.00 END ! the list of specific solvent-solvent pairs: NBFIX !Solvent molecule ! epsilon Rmin ! OT OT -0.15207 3.53650 HT OT -0.08363 1.99270 HT HT -0.04598 0.44900 END ! (of NBFIX) END ! (of parameters) read structure show * tip3p as solvent * ! read first the type of solvent sites SOLVENT nsite 3 ntype 2 OT OT type 1 segid BULK resnam TIP3 HT1 HT type 2 HT2 HT type 2 ! and the solvent geometry ZMATRIX OT HT1 OT 0.9572 HT2 OT 0.9572 HT1 104.52 ! now do the same for the solutes ! monoatomic molecules do not need a ZMATRIX since they do not have ! any geometry SOLUTE 1 nsite 1 ntype 1 CH31 CH31 type 1 segid SOLU resnam SOLU ! ! solute 2 is CH1E-CH1E, thus the two sites are of the same type ! SOLUTE 2 nsite 2 ntype 2 C1 CH31 type 1 segid SLU2 resnam SLU2 C2 CH32 type 1 ZMATRIX C1 C2 C1 4.0 END ! read the state (temperature, solvent density and cdie) state temp 298.15 density BULK 0.03334 cdie 78.6 ! read the converged cs(r) for the solvent-solvent (calculated ! before). open read unit 20 name tip3p-charmm.csr read cs(r) vv unit 20 close unit 20 ! iterate a few steps to check the convergence ! and generate the solvent-solvent g(r) iterate vv hnc ncycle 500 nprint 10 - tol 0.00001 rmix 0.39 ! now do the uv (solVent-solUte) calculation iterate uv hnc solute 1 ncycle 500 nprint 1 - init swi(1) 0.01 swf(1) 0.1 dsw(1) 0.01 - tol 0.9 rmix 0.39 iterate uv solute 1 hnc ncycle 500 nprint 1 - swi(1) 0.1 swf(1) 1.0 dsw(1) 0.1 - tol 0.9 rmix 0.39 iterate uv solute 1 hnc ncycle 5000 nprint 10 - tol 0.001 rmix 0.39 ! print out the solute-solvent g(r) characteristics analysis uv solute 1 ! write in files the distribution functions for the solute-solvent ! site pairs open write name soluv1-charmm.csr unit 20 write cs(r) uv solute 1 unit 20 * cs(r) for CH31 into water with the charmm-prepared executable * close unit 20 open write name soluv1-charmm.gr unit 20 write g(r) uv solute 1 unit 20 * g(r) for CH31 into water with the charmm-prepared executable * close unit 20 open write name soluv1-charmm-plt2.gr unit 20 write g(r) uv solute 1 plt2 all from 0.5 thru 10.0 - format(1x,10f10.5) unit 20 * g(r) for CH31 into tip3p water with the charmm-prepared executable * close unit 20 ! calculate the chemical potential and the solute-solvent ! interaction energy. The cavity energy cannot be calculated ! bewcause we have not done the derivative calculation. solvation chmpot energy plt2 verbose solute 1 ! =================================================================== ! now do the second solute calculation ------------------------------------ iterate uv hnc solute 2 ncycle 500 nprint 1 - init swi(1) 0.01 swf(1) 0.1 dsw(1) 0.01 - tol 0.9 rmix 0.39 iterate uv solute 2 hnc ncycle 500 nprint 1 - swi(1) 0.01 swf(1) 0.1 dsw(1) 0.01 - tol 0.9 rmix 0.39 iterate uv solute 2 hnc ncycle 5000 nprint 10 - tol 0.001 rmix 0.39 ! print out the solute-solvent g(r) characteristics analysis uv solute 2 ! write in files the distribution functions for the solute-solvent ! site pairs open write name soluv2-charmm.csr unit 20 write cs(r) uv solute 2 unit 20 * cs(r) for CH31-CH32 into water with the charmm-prepared executable * close unit 20 open write name soluv2-charmm.gr unit 20 write g(r) uv solute 2 unit 20 * g(r) for CH31-CH32 into water with the charmm-prepared executable * close unit 20 open write name soluv2-charmm-plt2.gr unit 20 write g(r) uv solute 2 plt2 all from 0.5 thru 10.0 - format(1x,10f10.5) unit 20 * g(r) for CH31-CH32 into tip3p water with the charmm-prepared executable * close unit 20 ! calculate the chemical potential and the solute-solvent ! interaction energy solvation chmpot energy plt2 verbose solute 2 ! =================================================================== ! now do the solute 1 - solute 2 calculation ! store the potential of mean force in us(r) iterate uu hnc w(r) solute 1 solute 2 ncycle 500 nprint 1 - init tol 0.001 rmix 0.29 open write name sol1-sol2.pmf unit 20 write us(r) uu solute 1 solute 2 unit 20 * pmf for the solutes CH3E and CH31-CH32 * close unit 20 open write name sol1-sol2.csr unit 20 write cs(r) uu solute 1 solute 2 unit 20 * cs(r) for the solutes CH3E and CH31-CH32 * close unit 20 ! =================================================================== ! now do the DERIVATIVE calculation ! test the calculation of the responce of the solvent to the ! solvation of a solute moleculte (infinite dilution) ! use tip3p water as solvent ! first for the solute 1 derivative hnc solute 1 ncycle 5000 nprint 1 - init tol 0.001 rmix 0.39 open write name tip3p-uv1-charmm.dcsr unit 30 write dc(r) solute 1 unit 30 * derivative of cs(r) of tip3p upon solvation of CH31 * close unit 30 open write name tip3p-uv1-charmm.dgr unit 30 write dg(r) solute 1 unit 30 * derivative of g(r) of tip3p upon solvation of CH31 * close unit 30 ! calculate the chemical potential, the interaction energy ! and the cavity formation energy solvation chmpot energy cavity solute 1 verbose ! now do the calculation for solute 2 derivative hnc solute 2 ncycle 5000 nprint 1 - init tol 0.001 rmix 0.39 open write name tip3p-uv2-charmm.dcsr unit 30 write dc(r) solute 2 unit 30 * derivative of cs(r) of tip3p upon solvation of CH31-CH32 * close unit 30 open write name tip3p-uv2-charmm.dgr unit 30 write dg(r) solute 2 unit 30 * derivative of g(r) of tip3p upon solvation of CH31-CH32 * close unit 30 ! calculate the chemical potential, the interaction energy ! and the cavity formation energy solvation chmpot energy cavity solute 2 verbose !exit RISM stop !exit CHARMM stop ----------------------------------------------------------------------

Information and HTML Formatting Courtesy of:

NIH/DCRT/Laboratory for Structural Biology

FDA/CBER/OVRR Biophysics Laboratory

Modified, updated and generalized by C.L. Brooks, III

The Scripps Research Institute