parameters-slvfe

Parameters for slvfe

The slvfe program has several parameters to change its behavior, specified by the file "parameters_fe" in the current directory.
The file can be specified in Fortran's namelist format.
The namelist group name is "fevars", so the parameters look like:

&fevars
clcond = "merge", ! Calculation type, "merge" / "basic" / "range"
numsln = 10,      ! Number of trajectory blocks in solution system
numref = 5,       ! Number of trajectory blocks in reference system
numdiv = 10,      ! Number of division for statistics, usually set equal to numsln

uvread = "yes",   ! "not" if average solute-solvent energy is calculated from engsln, instead of aveuv.tt
slfslt = "yes",   ! "not" if the solute self energy is not read
infchk = "yes",   ! Enable error analysis for the logarithmic-mesh part
inptemp = 300e0,  ! Input Temperature in Kelvin
/

An example parameters_fe file is included in the archive for version 0.2 and later.
The unit within the parameters_fe file is kcal/mol for energy, is Å for length, and K (Kelvin) for the temperature.

Description of each parameter

Before the description of the parameters, group and inft variables in the slvfe.F90 program are explained. These are described in the Appendix of J. Chem. Phys. 117, 3605 (2002) and correspond to the procedures for Eqs. (A5) and (A6), respectively. The variable group coarsens the energy meshes, andinft is to validate (or invalidate) the choice of the maximum energy mesh.

clcond

Type of handling the set of files. Three types are prepared: ‘basic’, ‘range’, and ‘merge’ (default)

• basic: takes one set of engsln.XX, engref.XX, and corref.XX and further takes group and inft parameters
• range: extended option with automatic examination of the mesh error. The group and inft variables are changed internally in the program. The integer parameter numprm determines how many variations are conducted, and the variable settings (group and inft) are described within the subroutine defcond in the program slvfe.F90. To change variable settings, open the source and modify numprm and the subroutine defcond.
• merge: (default) most extended option with automatic examination of the mesh error and treatment of multiple files. This option examines both the mesh error and statistical error

numprm

How many of group and inft sets are examined.
Active only when clcond = ‘range’ or ‘merge’

numsln

Number of engsln files.
Taken from the number in the soln directory as the default, and effective only when clcond = 'merge'

numref

Number of engref and corref files.
Taken from the number in the refs directory as the default, and effective only when clcond = 'merge'

numdiv

Number of division of the blocks in the soln run.
Set to be equal to numsln as the default, and effective only when clcond = 'merge'

ljlrc

Key for the long-range correction of the Lennard-Jones interaction between the solute and solvent. The default is 'not', and the long-range correction is performed when ljlrc is set to 'yes'. See Lennard-Jones long-range correction for the usage at ljlrc = 'yes' and a caution. Effective as of ver 0.3.5

avevolume

Average volume of the system. This value is necessary for the long-range correction of the Lennard-Jones interaction, and is to be set only when ljlrc = 'yes'. Effective as of ver 0.3.5

uvread

If ‘yes’, reading the average sum of solute-solvent interaction energy from a file. The default is ‘yes’, and the filename is soln/aveuv.tt when clcond is ‘merge’ (default) and the average sum vale needs to be input in the other clcond cases. If uvread = ‘not’, the average sum of solute-solvent interaction energy is constructed from engsln files. If ‘not’, the average sum will have some mesh error originating from the meshed distribution engsln. If ‘yes’, the average sum is free from the mesh error.

slfslt

Key for the self-energy correction to the solvation free energy and the average sum of solute-solvent interaction energy. If ‘yes’, the correction value is taken from refs/weight_refs. The default is ‘yes’, and is to be changed into 'not' when the periodic boundary condition is not employed in the parent MD.

normalize

If ‘yes’ (default), normalizing the engsln and engref files and enforcing consistency condition for corref file described in the Appendix C of J. Chem. Phys. 119, 9686-9702 (2003).

showdst

'not' is the default. If ‘yes’, showing some statistics of engsln and engref such as the minimum and maximum energies and the ratio of non-zero components

inptemp

Temperature of the system, taken as the default from the parent MD setup

pickgr

Identifying the group parameter to show the cumulative average in the last part of the slvfe output. The default value is 3

msemin

Minimum group parameter to examine the mesh error. The default = 1.

msemax

Maximum group parameter to examine the mesh error. The default = 5.

write_mesherror

If ‘not’, the mesh error is not shown.
If ‘yes’, the mesh error is shown at the end of the slvfe output.
Otherwise (default), the mesh error is not shown when it is smaller than mesherr defined below.
When the mesh error is larger than mesherr at the default setting of write_mesherror,
it is provided as an output in the following, two cases.
1) When the mesh error is larger than the 95% error given in the last line for cumulative average & 95% error for solvation free energy,
it is shown in the format of "Warning: mesh error is larger than 95% error"
2) When the mesh error is smaller than the 95% error,
it is shown in the format of "Warning: mesh error is larger than the threshold value of mesherr"
Case 1) precedes case 2), and in case 1), the mesh error is larger than both the 95% error and mesherr.
In case 2), the mesh error is smaller than the 95% error and it is larger than mesherr.
Case 2) provides the mesh error as an output only when mesherr is set to be positive (not an output when mesherr is equal to or less than 0).
Effective as of ver 0.3.7.

At ver 0.3.6, the key of write_mesherror works differently.
If ‘yes’, the mesh error is shown at the end of the slvfe output.
Otherwise (default), the mesh error is shown
1) when it is larger than the 95% error given in the last line for cumulative average & 95% error for solvation free energy
or 2) when the mesh error is smaller than the 95% error and it is larger than mesherr defined next.
Case 2) provides the mesh error as an output only when mesherr is set to be positive (not an output when mesherr is equal to or less than 0).

When the ERmod version is 0.3.5 or earlier, the mesh error is shown as a warning when it is larger than mesherr provided next.

mesherr

Threshold value to give a warning message of mesh error described above. The default setting is 0.1 kcal/mol.
Only at ver 0.3.6, the default is 0.

infchk

Key for specifying whether inft check is performed or not. The default is ‘not’

meshread

This parameter can be set to 'yes' only when infchk = 'yes' and the numbers of bins corresponding to the excluded-volume domain is read from soln/EngMesh; see Parameter files for ermod (ver 0.3) for EngMesh and also engmeshfile described below. Effective as of ver 0.3.5

solndirec

Key for specifying the directory for the data for the solution system. The default is ‘soln’. Effective as of ver 0.3.alpha5

refsdirec

Key for specifying the directory for the data for the reference solvent with insertion. The default is ‘refs’. Effective as of ver 0.3.alpha5

slndnspf

slncorpf

Keys for specifying the distribution function and correlation matrix for the solution. The default is slndnspf = 'engsln' and slncorpf = 'corsln'. Effective as of ver 0.3.alpha5

wgtslnfl

Keys for specifying the weight of each of the trajectory blocks for the solution run. The default is wgtslnfl = 'weight_soln'. Effective as of ver 0.3.alpha5

refdnspf

refcorpf

Keys for specifying the distribution function and correlation matrix for the reference solvent. The default is refdnspf = 'engref' and refcorpf = 'corref'. Effective as of ver 0.3.alpha5

wgtreffl

Keys for specifying the weight of each of the trajectory blocks for the reference-solvent run. The default is wgtreffl = 'weight_refs'. Effective as of ver 0.3.alpha5

aveuvfile

Key for specifying the name of the file storing the average sum of solute-solvent interaction energy (solvation energy). The default is aveuvfile = 'aveuv.tt'. Effective as of ver 0.3.alpha5

engmeshfile

Key for specifying the name of the EngMesh file which stores the user-defined meshes for energy. The default is engmeshfile = 'EngMesh'. Effective as of ver 0.3.5. See Parameter files for ermod (ver 0.3) for EngMesh

refmerge

As noted above for numsln and numdiv parameters, the soln run is divided into blocks and the corresponding block averages are treated as described in the section of Running slvfe: Getting Final Output of Quick Start Guide. When refmerge = 'yes' (default), the engref and corref files within the refs directory are summed (with the weights specified in weight_refs) and treated like single files when the slvfe program is executed. With refmerge = 'not', the refs run is also divided into numdiv blocks.

cumuint

cumuintfl

Key for providing the running integral as an output. The default is 'not' for cumuint, and cumuintfl is active only when cumuint = 'yes'.. See Running integral over the energy coordinate, and the estimation of the excluded-volume contribution for the usage at cumuint = 'yes''. Effective as of ver 0.3.7

extthres_soln

extthres_refs

When ¥rho is non-zero and ¥rho_0 is zero, ¥omega defined as -k_B T log(¥rho/¥rho_0) - ¥epsilon is determined through linear interpolation/extrapolation of the ¥omega values obtained in the domain of ¥rho > 0 and ¥rho_0 > 0. Since some of ¥rho and/or ¥rho_0 can be of bad statistics even when it is non-zero, the interpolation/extrapolation is done using the ¥omega values determined with ¥rho >= (value 1) and ¥rho_0 >= (value 2). In other words, ¥omega is subject to the interpolation/extrapolation when rho < (value 1) or ¥rho_0 < (value 2). In the above, (value 1) is set to extthres_soln ¥times (minimum, non-zero value of ¥rho numerically obtained), and (value 2) is extthres_refs ¥times (minimum, non-zero value of ¥rho_0 numerically obtained). The default is extthres_soln = 1 and extthres_refs = 1, and extthres_soln and/or extthres_refs is to be changed only for a purpose of numerical test. Effective as of ver 0.3.alpha5

minthres_soln

minthres_refs

The solvation free energy is computed through integration (summation) over the energy coordinate ¥epsilon. There may be a case that the numerical value of the integrand (summand) at some ¥epsilon is unphysical when ¥rho or ¥rho_0 is ill sampled at that ¥epsilon. With minthres_soln and minthres_refs, the summation is taken only over ¥epsilon with ¥rho > (value 1) and ¥rho_0 > (value 2), where (value 1) is set to minthres_soln ¥times (minimum, non-zero value of ¥rho numerically obtained) and (value 2) is minthres_refs ¥times (minimum, non-zero value of ¥rho_0 numerically obtained). The default is minthres_soln = 0 and minthres_refs = 0, and minthres_soln and/or minthres_refs is to be changed only for a purpose of numerical test. Effective as of ver 0.3.0

pecore

Number of logarithmic meshes. The default value is 200.
As of ver 0.3.4, this parameter is internally determined within the slvfe.f90 program and is not used any more.

peread

if ‘yes’, reading the number of meshes from a file. The default is ‘not’. If clcond is ‘merge’ (default), the filename in the case of peread = ‘yes’ needs to be soln/EcdInfo. If clcond = ‘basic’ or ‘range’, the filename needs to be input.
As of ver 0.3.4, the number of meshes is internally determined within the slvfe.f90 program and peread is not used any more.

ecdinfofl

Key for specifying the name of the file for the user-defined energy-coordinate mesh. The default is ecdinfofl = 'EcdInfo'. Effective as of ver 0.3.alpha5.
As of ver 0.3.4, the number of meshes is internally determined within the slvfe.f90 program and ecdinfofl is not used any more.