CHARMM c30b1 rism.doc



File: RISM ]-[ Node: Top
Up: (commands.doc) -=- Next: Syntax\n

          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\n

		   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
        ---




File: RISM ]-[ Node: Commands
Up: Syntax -=- Next: Theory -=- Previous: Syntax\n



		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.


=====================================================================





File: RISM ]-[ Node: Theory
Up: Syntax -=- Next: Examples -=- Previous: Commands\n




                  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.




File: RISM ]-[ Node: References
Up: Syntax -=- Next: Examples -=- Previous: Theory\n

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.






File: RISM ]-[ Node: Examples
Up: Syntax -=- Next: Top -=- Previous: References\n

 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

----------------------------------------------------------------------

CHARMM .doc Homepage


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