parameters-ermod02

Parameters for ermod (ver 0.2)

There are several parameters that control how the ermod program runs.
The followings are the parameters used in version 0.2,
though most of them are commonly used in version 0.3.

parameters_er

This file determines how the ermod program runs.
The file can be specified in Fortran's "namelist": http://www.cenapad.unicamp.br/parque/manuais/Xlf/lr96.HTM format.
The namelist group name is "ene_param" and "hist", and the parameters look as follows.
The unit within the parameters_er file is kcal/mol for energy and is Å for length.

&ene_param
        boxshp = 1,
        cltype = 2,
        ..........
        maxins = 10,
/
&hist
      eclbin=5.0e-2, ecfbin=2.0e-3, ec0bin=2.0e-4, finfac=10.0e0,
      ecdmin=-40.000000, ecfmns=-0.20e0, ecdcen=0.0e0, eccore=20.0e0,
      ecdmax=1.0e11, pecore=200
/

Each of the parameters is described below.

ene_param: Parameters for system setup and energy calculation

Some of the followings could have been modified.
Most up-to-date version is maintained in the comment lines in the engmain.F90 program.

engdiv : number of divisions of the total simulation length
maxins : maximum number of insertions for test solute particle, default = 1000
          This parameter is effective as an input only in calculation of reference solvent.
skpcnf : interval to skip the configuration examined
slttype : type of solute treatment
            1 : physical (solution)
            2 : test particle (reference solvent, rigid)
            3 : test particle (reference solvent, flexible)
sltpick : specifying the solute species
            1 <= sltpick <= numtype (default = 1) if slttype = 1
            sltpick = numtype if slttype >= 2
            This parameter is effective as an input only in calculation of solution.
refpick : specifying the mixed solvent species for superposition
            1 <= refpick <= numtype    when slttype = 1
            1 <= refpick <= numtype-1  when slttype >= 2
wgtslf : weighting by the self-energy  --- 0 : no  1 : yes
wgtins : weight of the solute intramolecular configuration
            0 : no  1 : yes (can be = 1 only when slttype = 3)
            If yes, a file called SltWght is separately prepared in the form of
                 (snapshot number, integer)  (weight, real)
            before ermod runs. 
estype : type of system
            1 : constant volume  2 : constant pressure
boxshp : shape of the unit cell box
            0 : non-periodic  1 : periodic and parallelepiped
inscnd : geometrical condition of the solute configuration
            0 : random  1 : spherical  2 : slab  3 : reference
inscfg : position and orientation for the inserted solute
            0 : only the intramolecular configuration is from the file
            1 : orientation is fixed from the file with random position
            2 : position and orientation are also fixed from the file
            The file for the solute configuration is SltInfo when slttype = 2
            and is SltConf when slttype = 3
          default = 0
hostspec : type of molecule forming host (micelle, membrane or protein)
            active only when inscnd is not equal to 0
            1 <= hostspec <= numtype    when slttype = 1
            1 <= hostspec <= numtype-1  when slttype >= 2
ljformat : input-file format for the LJ energy and length parameters
            0 : epsilon (kcal/mol) and sigma (A)
            1 : epsilon (kcal/mol) and Rmin/2 (A)
            2 : epsilon (kJ/mol) and sigma (nm)
            3 : A (kcal/mol A^12) and C (kcal/mol A^6)
            4 : C12 (kJ/mol nm^12) and C6 (kJ/mol nm^6)
          default = 1
lwreg : lower bound for the region of solute position
upreg : upper bound for the region of solute position 
        lwreg and upreg are effective only when inscnd is not equal to 0
elecut : cutoff of the real-space part of electrostatic interaction
lwljcut : lower limit of the LJ cutoff tapering function (switching function)
upljcut : upper limit of the LJ cutoff tapering function (switching function)
cmbrule : combination rule for LJ interaction
            0 : arithmetic mean is used for LJ sigma as for AMBER and CHARMM
            1 : geometric mean is used for LJ sigma as for OPLS
          default = 0
          geometric mean is always used for LJ epsilon
cltype : treatment of Coulomb interaction   0 : bare  1 : Ewald  2 : PME
          with the release of ver 0.2, the (full) Ewald is not supported any more 
          and so cltype = 1 is not active
screen : screening constant in Ewald summation
ewtoler : Ewald and PME tolerance to calculate the screen parameter
          When screen is given, screen has the priority
splodr : order of spline function used in PME
ms1max, ms2max, ms3max : number of meshes in PME along one direction
inptemp : temperature of the system in Kelvin
temp  : temperature of the system in kcal/mol
iseed : Random number seed. It determines where the solute is inserted in the reference system. 
    If iseed = 0, the seed is initialized based on current time. default = 0.

hist: Parameters defining the energy bins for the histogram

The energy bins are defined with 6 intervals.
1: coarse part, from the lowest energy to a small, negative energy
2: fine part, from the small, negative energy to a near-zero, negative energy
3: very fine part, from the near-zero, negative energy to a near-zero, positive energy
4: fine part, from the near-zero, positive energy to a small, positive energy
5: coarse part, from the small, positive energy to a large energy at which the dicretization is changed
6: logarithmic part, large energy region where the bin width is progressively increased exponentially

ecdmin : minimum value of the solute-solvent energy
ecfmns : smaller side of the finely discretized solute-solvent energy
ecmns0 : smaller side of the very finely discretized energy near ecdcen
ecdcen : central value of the energy coordinate, typically zero
ecpls0 : larger side of the very finely discretized energy near ecdcen
ecfpls : larger side of the finely discretized solute-solvent energy
eccore : the solute-solvent energy at which the discretization is changed
ecdmax : maximum value of the solute-solvent energy
eclbin : linear mesh for the solute-solvent energy
ecfbin : fine linear mesh for the solute-solvent energy
ec0bin : very fine linear mesh for the solute-solvent energy near zero
finfac : parameter to set the margin

The bin width is eclbin in intervals 1 and 5, is ecfbin in intervals 2 and 4, and is ec0bin in interval 3. In interval 6, the logarithmic interval is used

peread : determines whether the parameters are read from a separate file
     0 : parameters are read from param_eng
     1 : parameters are read separately from a file EcdInfo
    default = 0

Typically, it is fine to change only ecdmin if you encounter a trouble with an error message "The minimum of the energy coordinate is too large"; at this trouble, see Error: The minimum of the energy coordinate is too large.

MDinfo

System parameter file, which specifies the number of snapshots in the trajectory, the number of chemical species, the number of molecules for each species, and the number of atoms (interaction sites) within a molecule for each species.
An example case of ethylbenzene in water reads:

10000  2
2000   1
3     18

• 1st line: number of snapshot configurations and number of molecular species. In this case, 10000 snapshots are in the trajectory file and 2 chemical species are involved.
• 2nd line: number of molecules of each species. In this case, 2000 molecules for the first species and 1 molecule for the second species.
• 3rd line: number of sites within each solvent species. In this case, the first species are of 3 atoms (corresponds to water) and the second is of 18 atoms for ethylbenzene.

The number of snapshots in the 1st column of the 1st line is set automatically by running gen_input. It is set to the number of snapshots contained in the trajectory file. If you want to use part of the trajectory, you may open the MDinfo file and change manually the number of snapshots to the value you want to use (of course, your number needs to be smaller than the number of snapshots contained in the trajectory file).

MolPrmX and SltInfo

These files specifies interaction parameters (LJ and charge) for each atom.

For solute: SltInfo lists the atomic species and the interaction parameters
Example case:

 1  C  -0.1150  0.7000E-01  3.5500532
 2  H   0.1150  0.3000E-01  2.4200373
 3  C  -0.1150  0.7000E-01  3.5500532
…

• 1st column: numbering the atomic site
• 2nd column: element symbol for the atomic site
• 3rd column: partial charge on the site in the unit of elementary charge
• 4th column: LJ energy parameter \epsilon
• 5th column: LJ length parameter \sigma or Rmin/2

The units and format of the LJ energy and length parameters are specified by the ljformat parameter in parameters_er.
The default is that the energy parameter is the LJ \epsilon in the unit of kcal/mol and that the length parameter is the Rmin/2 in the unit of Å.
The above example is expressed with the LJ \epsilon in the unit of kcal/mol and the LJ \sigma in the unit of Å, corresponding to the standard expression of 4 \epsilon {(\sigma/r)^12 -(\sigma/r)^6}.
In this case, it is necessary to set ljformat = 0.

For solvent species: MolPrm1, MolPrm2 …
For the 1st solvent species MolPrm1
For the 2nd solvent species MolPrm2
Example for (CHARMM-modified) TIP3P water:

1 O   -0.8340   0.1521   3.1506
2 H    0.4170   0.0460   0.4000
3 H    0.4170   0.0460   0.4000

The format is the same as SltInfo described above.

Only when the system is the reference solvent with test-particle insertion of rigid solute, SltInfo has a different format.

1  C 　-0.115   7.00E-02  3.5500532  1.457  0.477  -18.403
2  H   0.115   3.00E-02  2.4200373   2.345  0.202  -17.853
3  C   -0.115  7.00E-02  3.5500532   0.268  -0.215  -18.094 
…

The formats in 1st-5th columns are identical to those described above.
The 6th-8th columns are the intramolecular (x, y, z) coordinate in the unit of Å.
The center-of-mass position or orientation does not need to be “standardized”.
For example, the center of mass needs not to be set to (0,0,0).
When the solute is rigid, the 6th-8th columns of SltInfo are all needed to specify the solute structure. When the solute is flexible, on the other hand, the information on the solute structure is contained in the SltConf file.

The file format of MolPrmX and SltInfo is shown in the ljformat in the parameters_er file.
The convention corresponding to each setting of ljformat is described above in the section of parameters_er.

EcdInfo

If user wants to specify a different binning strategy for each chemical species, EcdInfo is to be used.
EcdInfo is used only when "peread=1" is specified in "hist"§ion in parameters_er.
Both soln and refs should use the same EcdInfo (otherwise there may exist a risk to silently corrupt the result).
User must also specify "peread='yes'" in the parameters_fe file.
Typical format for EcdInfo reads as

species  eclbin ecfbin ec0bin finfac ecdmin ecfmns ecdcen eccore ecdmax pecore
0        1.0e-3 1.0e-3 1.0e-3 1.0e0   -179.0 -177.5 -176.5 -175.0
1        5.0e-1 5.0e-2 5.0e-3 10.0e0 -40.0  -5.0   0.0   20.0   1.0e11 200
3        5.0e-1 5.0e-2 5.0e-3 10.0e0 -60.0  -10.0   0.0   20.0   1.0e11 500
5        5.0e-2 2.0e-3 2.0e-4 10.0e0 -40.0  -0.20e0 0.0e0 20.0e0 1.0e11 200

with the convention that the energy is expressed in kcal/mol.

The first line is reserved for comments.
From the second line on, each lists the values of the binning parameters shown in the first line; see the "hist" section above in this page for the description of the parameters.
On the second line, the binning parameters for self interaction energy is listed.
On the third line and after, the binning parameters for each solvent species are specified.
Only on the 2nd line (i.e. species 0, self interaction), there are no entries in the 10 and 11th columns ("ecdmax" and "pecore" sections) and the histogram is not constructed for the exponentially growing region.
This feature is useful for self interaction energy, where the energy variation is typically weak.
The first column identifies the solvent species (0 in the case of solute self).
In the above example, the species 2 and 4 are absent.
For those species which are absent in EcdInfo, the binning parameters are simply taken from parameters_er.
In this sense, parameters_er provides a "default" set of binning parameters for all the species, and only those species particularly cared need to be listed in EcdInfo.
When the binning parameters are given, the energy meshes are constructed through the procedure provided within the enginit subroutine of the engproc.F90 program.