Recent changes to parameters-erdst

parameters-erdst modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Mon, 10 Nov 2025 10:27:00 -0000

--- v106
+++ v107
@@ -469,7 +469,7 @@

 ~~~~
 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
+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

parameters-erdst modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Mon, 10 Nov 2025 10:25:35 -0000

--- v105
+++ v106
@@ -465,12 +465,7 @@
 EcdInfo
 ----

-The parameters within the **hist** section of parameters_er can be speficied differently for different species.
-For this purpose, user prepares EcdInfo.
-It is used only when ecprread = 1 or peread = 1 is specified in the **hist** section of parameters_er;
-the ecprread parameter is available as of ver 0.3.5 and only peread can be used when the version is 0.3.4 or earlier.
-Both soln and refs should use the same EcdInfo (otherwise there may exist a risk to silently corrupt the result).
-Typical format for EcdInfo reads as
+The parameters within the **hist** section of parameters_er can be speficied differently for different species. For this purpose, user prepares EcdInfo. It is used only when ecprread = 1 or peread = 1 is specified in the **hist** section of parameters_er; the ecprread parameter is available as of ver 0.3.5 and only peread can be used when the version is 0.3.4 or earlier. Both soln and refs should use the same EcdInfo (otherwise there may exist a risk to silently corrupt the result). Typical format for EcdInfo reads as

 ~~~~
 species  eclbin ecfbin ec0bin finfac ecdmin ecfmns ecdcen eccore ecdmax pecore
@@ -491,18 +486,14 @@
 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.
+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.
 It should be noted, in addition, that unless selfcal = 1, the line with species = 0 is not necessary to be written or is simply ignored even if it is written in EcdInfo.

 EcdMesh
 ----

-User-defined meshes can be introduced, and to do so, user prepares EcdMesh.
-It is used only when meshread = 1 is specified in the **hist** section of parameters_er.
-Both soln and refs should use the same EcdMesh (otherwise there may exist a risk to silently corrupt the result).
-Typical format for EcdMesh reads as
+User-defined meshes can be introduced, and to do so, user prepares EcdMesh. It is used only when meshread = 1 is specified in the **hist** section of parameters_er. Both soln and refs should use the same EcdMesh (otherwise there may exist a risk to silently corrupt the result). Typical format for EcdMesh reads as

 ~~~~
 0  100

parameters-erdst modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Thu, 12 Dec 2024 10:33:06 -0000

--- v104
+++ v105
@@ -60,12 +60,12 @@
             0 (default) : 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. 
+            before erdst runs. 
 wgtsys : weight of a trajectory snapshot of the solution or (reference-)solvent system
             0 (default) : no   1 : yes
             If yes, a file called SysWght is separately prepared in the form of
                  (snapshot number, integer)  (weight, real)
-            before ermod runs.
+            before erdst runs.
 boxshp : shape of the unit cell box
             0 : non-periodic  1 : periodic and parallelepiped
 estype : type of system
@@ -99,7 +99,7 @@
             2 : spherically random position with radius specified from lwreg to upreg as
                  r = com(aggregate) + dr with lwreg < dr < upreg
                  The species forming the aggregate is defined by hostspec
-                 The ermod program does not take care of
+                 The erdst program does not take care of
                      the periodic boundary condition concerning the location of the aggregate.
                  During the simulation, the center of the aggregate
                      should be restrainined around the center of the simulation cell
@@ -109,7 +109,7 @@
                 slab geometry specified as z = com(aggregate) + dz with
                 lwreg < dz < upreg for rectangular box periodic condition.
                 The species forming the aggregate is defined by hostspec
-                The ermod program does not take care of
+                The erdst program does not take care of
                      the periodic boundary condition concerning the location of the aggregate.
                 During the simulation, the z-coordinate of the center of the aggregate
                      should be restrainined around the z-center of the simulation cell
@@ -122,7 +122,7 @@
                 -upreg < dz < -lwreg or lwreg < dz < upreg
                 for rectangular box periodic condition.
                 The species forming the aggregate is defined by hostspec
-                The ermod program does not take care of
+                The erdst program does not take care of
                      the periodic boundary condition concerning the location of the aggregate.
                 During the simulation, the z-coordinate of the center of the aggregate
                      should be restrainined around the z-center of the simulation cell
@@ -138,7 +138,7 @@
                 The reference structure needs be given as RefInfo in PDB format.
                 RefInfo contains the structure of the host species (species forming
                      the reference host is defined by refspec) followed by the solute structure
-                The ermod program does not take care of the periodic boundary condition
+                The erdst program does not take care of the periodic boundary condition
                      concerning the location of the reference structure.
                 During the simulation, the center of the reference species
                      should be restrainined around the center of the simulation cell
@@ -158,7 +158,7 @@
                 (species forming the reference host is defined by refspec)
                  followed by the solute structure 
        In ver 0.3.4 and the previous versions, the default is insorigin = 0
-              and the ermod program halts with an error message
+              and the erdst program halts with an error message
               when insposition = 0 and insorigin /= 0,
               when insposition = 1 and insorigin /= 1, when insorigin = 1 and insposition /= 1,
               when insposition = 2, 3 or 4 and insorigin /= 2, when insorigin = 2 and insposition /= 2, 3 or 4
@@ -259,7 +259,7 @@

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.
-In fact, ecmns0, ecpls0, and ecfpls are internally set in ermod and and cannot be changed in parameters_er
+In fact, ecmns0, ecpls0, and ecfpls are internally set in erdst and and cannot be changed in parameters_er

It is also possible to specify a different binning strategy for each species. Keys for doing so are

@@ -281,7 +281,7 @@

when the version is 0.3.4 or earlier.
-At ver 0.3.5, peread is deprecated and is read as ecprread within the ermod program.
+At ver 0.3.5, peread is deprecated and is read as ecprread within the erdst program.
See below for the descriptions of EcdInfo and EcdMesh.

Typically, it is fine to change only ecdmin if user encounters 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.

parameters-erdst modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Thu, 08 Aug 2024 03:39:29 -0000

--- v103
+++ v104
@@ -533,12 +533,12 @@
 The first line for each species provies the numbers of meshes.
 The second column is the total number of bins for the species in the first column, and the third column is the number of bins corresponding to the excluded-volume domain.
 The value in the third column corresponds to the pecore parameters in parameters_er and EcdInfo.
-When the value in the second column is not larger than the value in the third, the ermod run halts with an error message.
+When the value in the second column is not larger than the value in the third, the erdst run halts with an error message.
 From the second and subsequent lines for each species, the format is
 ~~~~
 (species, integer)  (bin number, integer)   (energy mesh, real)
 ~~~~
-The total number of lines specifying the energy meshes for a given species needs to be the same as the total number of meshes specifed by the second column of the first line for that species; when they are not the same, ermod halts with an error message.
+The total number of lines specifying the energy meshes for a given species needs to be the same as the total number of meshes specifed by the second column of the first line for that species; when they are not the same, erdst halts with an error message.
 The energy mesh should be written in ascending order, and its value in EcdMesh is the lower limit of the bin.
 When the i-th and (i+1)-th meshes are a(i) and a(i+1), respectively, a datum x is counted in the i-th bin when a(i) <= x < a(i+1)

@@ -548,8 +548,8 @@
 PermIndex
 ----

-User can change the ordering of the atoms in the trajectory from the parent simulation when it is fed to ermod.
-When a PermIndex file is present in the directory where ermod is run,
+User can change the ordering of the atoms in the trajectory from the parent simulation when it is fed to erdst.
+When a PermIndex file is present in the directory where erdst is run,
 the atom number is subject to permutation through the correspondence of
 ~~~~
 1   1
@@ -562,23 +562,23 @@
 ~~~~
 for example.
 This is the format of PermIndex,
-and the entries in the first and second columns are the atom numbers in the trajectory from the parent simulation and in the ermod run, respectively.
+and the entries in the first and second columns are the atom numbers in the trajectory from the parent simulation and in the erdst run, respectively.
 In the above example, the 1st to 6th atoms in the parent trajectory
-are treated as 1st, 2nd, 3rd, 11th, 12th, and 13th atoms in ermod, respectively.
+are treated as 1st, 2nd, 3rd, 11th, 12th, and 13th atoms in erdst, respectively.
 There are no changes in the number ordering for those atoms which are not listed,
 and thus, the first three lines are actually not necessary in the example.

 The permutation functionality is convenient to re-group the atoms.
-For example, the molecules of the same species are supposed to appear consecutively as a block in ermod.
+For example, the molecules of the same species are supposed to appear consecutively as a block in erdst.
 If user has 500 H2O and 100 ETOH molecules,
-a single snapshot configuration of the trajectory fed to ermod
+a single snapshot configuration of the trajectory fed to erdst
 should have the coordinates of 500 H2O molecules first and of 100 ETOH second.
 The coordinates of H2O and ETOH are not to be mixed together,
 and the numbering within each species needs to be always the same, in addition;
 the H2O coordinates can saved in any order of OHH, HOH, or HHO,
 while only a single order is used throughout all the H2O molecules.
 A trajectory file from the simulation may not conform to the above conventions, however.
-In such a case, the atom numbers are modified by PermIndex so that they are appropriate for an ermod run,
+In such a case, the atom numbers are modified by PermIndex so that they are appropriate for an erdst run,
 and it may also be necessary to rewrite **MDinfo** and **MolPrmX** manually as illustrated next.

 When a polymer is seen as a collection of segments and each segment is treated as a "solvent" species,

parameters-erdst modified by Shun Sakuraba

Shun Sakuraba — Thu, 11 Apr 2024 10:08:12 -0000

--- v102
+++ v103
@@ -325,8 +325,8 @@

 * 1st column: numbering the atomic site
 * 2nd column: mass for the atomic site
-* 3rd column: atomtype  (unused in ERmod)
-* 4th column: atomname  (unused in ERmod)
+* 3rd column: atomtype  (unused in ERmod; in LAMMPS this is number)
+* 4th column: atomname  (unused in ERmod; in LAMMPS this is "None")
 * 5th column: partial charge on the site in the unit of elementary charge
 * 6th column: LJ energy parameter \epsilon
 * 7th column: LJ length parameter \sigma or Rmin/2

parameters-erdst modified by Shun Sakuraba

Shun Sakuraba — Thu, 11 Apr 2024 09:06:24 -0000

--- v101
+++ v102
@@ -356,11 +356,11 @@
 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 (ver1.0 uses new one).
+1 15.9994   OW    O     -0.8340   0.1521   3.1506
+2  1.0080   HW    H1     0.4170   0.0460   0.4000
+3  1.0080   HW    H2     0.4170   0.0460   0.4000
+~~~~
+The format is the same as SltInfo described above (similar to `SltInfo`, ver0.3 uses shorter notation).

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

@@ -398,23 +398,25 @@
 When ljformat = 5, the format of MolPrmX and SltInfo is different from the one described above and reads

 ~~~~
-      1   O   -0.67180    1 0
-      2   H    0.41430    2 0
-      3   C    0.31180    3 0
-      4   H   -0.02940    4 0
-      5   H   -0.02940    4 0
+      1   15.9994 OH  O1    -0.67180    1 0
+      2   1.008   HO  H1     0.41430    2 0
+      3   12.0110 CT  C1     0.31180    3 0
+      4   1.008   HT  H11   -0.02940    4 0
+      5   1.008   HT  H12   -0.02940    4 0
 …
 ~~~~

 * 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 interaction type
-* 5th column: dummy (no information contained).
-
-The 1st to 3rd columns have the same formats as those described above, and are to be prepared as such.
-The 4th column is an integer specifying the LJ interaction type of the atom.
-The 5th column contains no information and is simply there as a dummy.
+* 2nd column: mass for the atomic site
+* 3rd column: atom type (unused)
+* 4th column: atom name (unused)
+* 5th column: partial charge on the site in the unit of elementary charge
+* 6th column: LJ interaction type
+* 7th column: dummy (no information contained).
+
+The 1st to 5th columns have the same formats as those described above, and are to be prepared as such.
+The 6th column is an integer specifying the LJ interaction type of the atom.
+The 7th column contains no information and is simply there as a dummy.

 The LJ interaction parameter sets are stored in the LJTable file in the example format of

parameters-erdst modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Thu, 11 Apr 2024 08:50:03 -0000

--- v100
+++ v101
@@ -364,6 +364,14 @@

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

+(Version 1.0)
+~~~~
+1  12.0001 CA   C1 　-0.115   7.00E-02  3.5500532  1.457  0.477  -18.403
+2  1.0008  HA   H1    0.115   3.00E-02  2.4200373   2.345  0.202  -17.853
+3  12.0001 CA   C2   -0.115  7.00E-02  3.5500532   0.268  -0.215  -18.094 
+…
+~~~~
+(Version <=0.3)
 ~~~~
 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
@@ -371,19 +379,11 @@
 …
 ~~~~

-(After ver 1.0:)
-~~~~
-1  12.0001 CA   C1 　-0.115   7.00E-02  3.5500532  1.457  0.477  -18.403
-2  1.0008  HA   H1    0.115   3.00E-02  2.4200373   2.345  0.202  -17.853
-3  12.0001 CA   C2   -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 formats in 1st-7th (1st-5th for Version <=0.3) columns are identical to those described above.
+The 8th-10th (6th-8th for Version <=0.3) 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.
+When the solute is rigid, the 8th-10th 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.

parameters-erdst modified by Shun Sakuraba

Shun Sakuraba — Thu, 11 Apr 2024 04:05:02 -0000

parameters-ermod03 modified by Shun Sakuraba

Shun Sakuraba — Thu, 11 Apr 2024 04:04:45 -0000

--- v98
+++ v99
@@ -1,13 +1,13 @@
-Parameters for ermod (ver 0.3)
+Parameters for erdst (Ver 1.0) or ermod (Ver 0.3)
 ====

-There are several parameters that control how the ermod program runs.
-The followings are the parameters used in version 0.3, though many of them are commonly used in version 0.2.
+There are several parameters that control how the erdst / ermod program runs.
+The followings are the parameters used in version 1.0, though many of them are commonly used in version 0.3

 parameters_er
 ----

-This file determines how the ermod program runs.
+This file determines how the erdst 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.
@@ -315,6 +315,23 @@
 For solute: SltInfo lists the atomic species and the interaction parameters
 Example case:

+(Version 1.0)
+~~~~
+ 1  12.0001   CA     C1      -0.1150  0.7000E-01  3.5500532
+ 2  1.0008    HA     H1       0.1150  0.3000E-01  2.4200373
+ 3  12.0001   CA     C2      -0.1150  0.7000E-01  3.5500532
+…
+~~~~
+
+* 1st column: numbering the atomic site
+* 2nd column: mass for the atomic site
+* 3rd column: atomtype  (unused in ERmod)
+* 4th column: atomname  (unused in ERmod)
+* 5th column: partial charge on the site in the unit of elementary charge
+* 6th column: LJ energy parameter \epsilon
+* 7th column: LJ length parameter \sigma or Rmin/2
+
+(Version <=0.3)
 ~~~~
  1  C  -0.1150  0.7000E-01  3.5500532
  2  H   0.1150  0.3000E-01  2.4200373
@@ -343,7 +360,7 @@
 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.
+The format is the same as SltInfo described above (ver1.0 uses new one).

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

@@ -351,6 +368,14 @@
 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 
+…
+~~~~
+
+(After ver 1.0:)
+~~~~
+1  12.0001 CA   C1 　-0.115   7.00E-02  3.5500532  1.457  0.477  -18.403
+2  1.0008  HA   H1    0.115   3.00E-02  2.4200373   2.345  0.202  -17.853
+3  12.0001 CA   C2   -0.115  7.00E-02  3.5500532   0.268  -0.215  -18.094 
 …
 ~~~~

parameters-ermod03 modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Sat, 14 Jan 2023 02:14:56 -0000

--- v97
+++ v98
@@ -515,7 +515,7 @@
 The energy mesh should be written in ascending order, and its value in EcdMesh is the lower limit of the bin.
 When the i-th and (i+1)-th meshes are a(i) and a(i+1), respectively, a datum x is counted in the i-th bin when a(i) <= x < a(i+1)

-For those species which are absent in EcdInfo, the binning parameters are taken from parameters_er or EcdInfo.
+For those species which are absent in EcdMesh, the binning parameters are taken from parameters_er or EcdInfo.


 PermIndex