3D-RISM

&rism namelist variables¶

xvv (Default = "tip3p")

Define the selected solvent for 3D-RISM. These solvent xvv files are contained in xBFreE, but you can define a new one simply adding the file path.

• tip3p
• spc
• spc-nacl-3
• spc_mmpbsa_py

Closure approximations¶

closure (Default = "kh")

Comma separate list of closure approximations. If more than one closure is provided, the 3D-RISM solver will use the closures in order to obtain a solution for the last closure in the list when no previous solutions are available. The solution for the last closure in the list is used for all output. The use of several closures combined with different tolerances can be useful to overcome convergence issues (see §7.3.1)

• "kh": Kovalenko-Hirata
• "hnc": Hyper-netted chain equation
• "psen": Partial Series Expansion of order-n where “n” is a positive integer (e.g., "pse3")

Examples

One closureSeveral closures

 closure = pse3

 closure = kh, pse3

Solvation free energy corrections¶

gfcorrection (Default = 0)

Compute the Gaussian fluctuation excess chemical potential functional. See §7.1.2

• 0: Off
• 1: On

pcpluscorrection (Default = 0)

Compute the PC+/3D-RISM excess chemical potential functional. See §7.2.4

• 0: Off
• 1: On

Long-range asymptotics¶

noasympcorr (Default = 1)

Use long-range asymptotic corrections for thermodynamic calculations.

• 0: Do not use long-range corrections
• 1: Use the long-range corrections

treeDCF (Default = 1)

Use direct sum, or the treecode approximation to calculate the direct correlation function long-range asymptotic correction.

• 0: Use direct sum
• 1: Use treecode approximation

treeTCF (Default = 1)

Use direct sum, or the treecode approximation to calculate the total correlation function long-range asymptotic correction.

• 0: Use direct sum
• 1: Use treecode approximation

treeCoulomb (Default = 1)

Use direct sum, or the treecode approximation to calculate the Coulomb potential energy.

• 0: Use direct sum
• 1: Use treecode approximation

treeDCFMAC (Default = 0.1)

Treecode multipole acceptance criterion for the direct correlation function long-range asymptotic correction.

treeTCFMAC (Default = 0.1)

Treecode multipole acceptance criterion for the total correlation function long-range asymptotic correction.

treeCoulombMAC (Default = 0.1)

Treecode multipole acceptance criterion for the Coulomb potential energy.

treeDCFOrder (Default = 2)

Treecode Taylor series order for the direct correlation function long-range asymptotic correction.

treeTCFOrder (Default = 2)

Treecode Taylor series order for the total correlation function long-range asymptotic correction. Note that the Taylor expansion used does not converge exactly to the TCF long-range asymptotic correction, so a very high order will not necessarily increase accuracy.

treeCoulombOrder (Default = 2)

Treecode Taylor series order for the Coulomb potential energy.

treeDCFN0 (Default = 500)

Maximum number of grid points contained within the treecode leaf clusters for the direct correlation function long-range asymptotic correction. This sets the depth of the hierarchical octtree.

treeTCFN0 (Default = 500)

Maximum number of grid points contained within the treecode leaf clusters for the total correlation function long-range asymptotic correction. This sets the depth of the hierarchical octtree.

treeCoulombN0 (Default = 500)

Maximum number of grid points contained within the treecode leaf clusters for the Coulomb potential energy. This sets the depth of the hierarchical octtree.

Solvation box¶

Variable box size¶

buffer (Default = 14)

Minimum distance (in Å) between solute and edge of solvation box. Specify this with grdspc below. Mutually exclusive with ng and solvbox. See §7.2.3 for details on how this affects numerical accuracy and how this interacts with ljTolerance, and tolerance

• when < 0: Use fixed box size (see ng and solvbox below)
• when >= 0: Use buffer distance

grdspc(Default = 0.5,0.5,0.5)

Grid spacing (in Å) of the solvation box. Specify this with buffer above. Mutually exclusive with ng and solvbox.

Fixed box size¶

ng (Default = -1,-1,-1)

Comma separated number of grid points to use in the x, y, and z directions. Used only if buffer < 0. Mutually exclusive with buffer and grdspc above, and paired with solvbox below.

Warning

No default, this must be set if buffer < 0. As a general requirement, the number of grids points in each dimension must be divisible by two, and the number of grid points in the z-axis must be divisible by the number of processes.

As an example: define like ng=1000,1000,1000, where all numbers are divisible by two and you can use 1, 2, 4, 5, 8, 10... pocessors, all divisors of 1000 (value in the z-axis).

Take into account that at a certain level, running RISM in parallel may actually hurt performance, since previous solutions are used as an initial guess for the next frame, hastening convergence. Running in parallel loses this advantage. Also, due to the overhead involved in which each thread is required to load every topology file when calculating energies, parallel scaling will begin to fall off as the number of threads reaches the number of frames.

solvbox (Default = -1,-1,-1)

Sets the size in Å of the fixed size solvation box. Used only if buffer < 0. Mutually exclusive with buffer and grdspc above, and paired with ng above.

Warning

No default, this must be set if buffer < 0. Define like solvbox=20,20,20

solvcut (Default = 14)

Cutoff used for solute-solvent interactions. The default value is that of buffer. Therefore, if you set buffer < 0 and specify ng and solvbox instead, you must set solvcut to a nonzero value; otherwise the program will quit in error.

Solution convergence¶

tolerance (Default = 0.00001)

A comma-separated list of maximum residual values for solution convergence. This has a strong effect on the cost of 3D-RISM calculations (smaller value for tolerance -> more computation). When used in combination with a list of closures it is possible to define different tolerances for each of the closures. This can be useful for difficult to converge calculations (see §7.4.1). For the sake of efficiency, it is best to use as high a tolerance as possible for all but the last closure. See §7.2.3 for details on how this affects numerical accuracy and how this interacts with ljTolerance, buffer, and solvbox. Three formats of list are possible:

• one tolerance: All closures but the last use a tolerance of 1. The last tolerance in the list is used by the last closure. In practice this is the most efficient.
• two tolerances: All closures but the last use the first tolerance in the list. The last tolerance in the list is used by the last closure.
• n tolerances: Tolerances from the list are assigned to the closure list in order.

Examples

One closure/One toleranceSeveral closures/One toleranceSeveral closures/Two tolerancesSeveral closures/Several tolerances

closure = pse3, tolerance=0.00001

A tolerance of 0.00001 will be used for clousure pse3

 closure = kh, pse3, tolerance=0.00001

A tolerance of 1 will be used for clousure kh, while 0.00001 will be used for clousure pse3. Equivalent to closure = kh, pse3, tolerance=1,0.00001

 closure = kh, pse2, pse3, tolerance=0.01, 0.00001

A tolerance of 0.01 will be used for clousures kh and pse2, while 0.00001 will be used for clousure pse3. Equivalent to closure = kh, pse2, pse3, tolerance=0.01,0.01,0.00001

 closure = kh,pse2,pse3, tolerance=0.1,0.01,0.00001

A tolerance of 0.1 will be used for clousure kh, 0.01 will be used for clousure pse2, while 0.00001 will be used for clousure pse3.

ljTolerance (Default = -1)

Lennard-Jones accuracy (Optional.) Determines the Lennard-Jones cutoff distance based on the desired accuracy of the calculation. See §7.2.3 for details on how this affects numerical accuracy and how this interacts with tolerance, buffer, and solvbox.

asympKSpaceTolerance (Default = -1)

Tolerance reciprocal space long range asymptotics accuracy (Optional.) Determines the reciprocal space long range asymptotic cutoff distance based on the desired accuracy of the calculation. See §7.2.3 for details on how this affects numerical accuracy. Possible values are:

• when < 0: asympKSpaceTolerance = tolerance/10
• when = 0: no cutoff
• when > 0: given value determines the maximum error in the reciprocal-space long range asymptotics calculations

mdiis_del (Default = 0.7)

MDIIS step size.

mdiis_nvec (Default = 5)

Number of previous iterations MDIIS uses to predict a new solution.

mdiis_restart (Default = 10)

If the current residual is mdiis_restart times larger than the smallest residual in memory, then the MDIIS procedure is restarted using the lowest residual solution stored in memory. Increasing this number can sometimes help convergence.

maxstep (Default = 10000)

Maximum number of iterations allowed to converge on a solution.

npropagate (Default = 5)

Number of previous solutions propagated forward to create an initial guess for this solute atom configuration.

• =0: Do not use any previous solutions
• = 1..5: Values greater than 0 but less than 4 or 5 will use less system memory but may introduce artifacts to the solution (e.g., energy drift).

Output¶

polardecomp (Default = 0)

Decomposes solvation free energy into polar and non-polar components. Note that this typically requires 80% more computation time.

• 0: Don’t decompose solvation free energy into polar and non-polar components.
• 1: Decompose solvation free energy into polar and non-polar components.

entropicdecomp (Default = 0)

Decomposes solvation free energy into energy and entropy components. Also performs temperature derivatives of other calculated quantities. Note that this typically requires 80% more computation time and requires a .xvv file version 1.000 or higher (available within GMXMMPBSA data folder). See §7.1.3 and §7.3

• 0: No entropic decomposition
• 1: Entropic decomposition

rism_verbose (Default = 0)

Level of output in temporary RISM output files. May be helpful for debugging or following convergence.

• 0: just print the final result
• 1: additionally prints the total number of iterations for each solution
• 2: additionally prints the residual for each iteration and details of the MDIIS solver (useful for debugging and convergence analyses)