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parameters-erdst
Parameters for erdst (Ver 1.0) or ermod (Ver 0.3)
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 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.
&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
example:
skpcnf = 1 (default): all the configurations within the HISTORY are analyzed.
skpcnf = 2: every other configuration within HISTORY is analyzed.
skpcnf = 10: every 10 configuration within HISTORY is analyzed.
corrcal : calculation of the correlation matrix
0 : no calculation 1 : calculation performed
default = 0 when slttype = 1 (solution system)
default = 1 when slttype = 2 or 3 (reference solvent system)
selfcal : construction of the self-energy distribution
0 (default) : no construction 1 : constructed
slttype : type of solute treatment
1 : physical (solution)
2 : test particle (reference solvent, rigid)
3 : test particle (reference solvent, flexible)
wgtslf : weighting by the self-energy --- 0 : no 1 : yes
default = 0 in soln and in refs without Ewald or PME
default = 1 in refs with Ewald or PME
wgtins : weight of the solute intramolecular configuration
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 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 erdst runs.
boxshp : shape of the unit cell box
0 : non-periodic 1 : periodic and parallelepiped
estype : type of system
1 : constant volume 2 : constant pressure
sltspec : specifying the solute species
1 <= sltspec <= numtype (default = 1) when slttype = 1
sltspec = numtype when slttype >= 2
This parameter is effective as an input only in soln calculation.
hostspec : solvent spcies to act as a host and bind the guest solute
(micelle, membrane or protein)
1 <= hostspec <= numtype when slttype = 1
1 <= hostspec <= numtype - 1 when slttype >= 2
This parameter is effective as an input only when insposition = 2, 3, or 4
See also the description for insposition
As of ver 0.3.2, more than a single species can be set, for example, by writing
hostspec = 1 2,
refspec : specifying the mixed solvent species for superposition reference
1 <= refspec <= numtype when slttype = 1
1 <= refspec <= numtype - 1 when slttype >= 2
This parameter is effective as an input only when insposition = 5
See also the description for insposition
As of ver 0.3.2, more than a single species can be set, for example, by writing
refspec = 2 3,
sltpick (deprecated) : same as sltspec
refpick (deprecated) : same as refspec
insposition : position for the solute
0 (default) : fully random position (within perodic bondary)
1 : no position change from the value in the file to be read
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 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
or after the simulation, the trajectory is displaced so that
the center of the aggregate is around the center of the cell.
3 : slab random position (generic case)
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 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
or after the simulation, the trajectory is displaced so that
the z-center of the aggregate is around the z-center of the cell.
Positioning is more complicated in parallelpiped cell.
(see insertion.F90)
4 : slab random position (symmetric bilayer)
slab geometry specified as z = com(aggregate) + dz with
-upreg < dz < -lwreg or lwreg < dz < upreg
for rectangular box periodic condition.
The species forming the aggregate is defined by hostspec
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
or after the simulation, the trajectory is displaced so that
the z-center of the aggregate is around the z-center of the cell.
Positioning is more complicated in parallelpiped cell.
(see insertion.F90)
5 : random position relative to a reference structure
The solvent species identified with the refspec parameter is set to
the reference structure accompanying the reference position of solute insertion
and the solute is placed relative to that reference
with condition of lwreg < RMSD < upreg
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 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
or after the simulation, the trajectory is displaced so that
the center of the reference species is around the center of the cell.
insorigin : translational origin of the solute position
As of ver 0.3.5, the value of insorigin is set internally from the value of insposition
to 0 when insposition = 0, to 1 when insposition = 1,
to 2 when insposition = 2, 3 or 4, and to 3 when insposition = 5
0 : mass weighted center is moved to (0, 0, 0)
1 : no COM change from the value in the file to be read
2 : mass weighted center is moved to aggregate center
(species forming the aggregate is defined by hostspec)
3 : fit to reference structure.
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
In ver 0.3.4 and the previous versions, the default is insorigin = 0
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
when insposition = 5 and insorigin /= 3, or when insorigin = 3 and insposition /= 5
insorient : orientation for the solute
0 (default) : random orientation
1 : no orientation change from the value in the file to be read
insstructure : intramolecular structure of the solute
0 (default) : no restriction, used as is from trajectory or file
1 : only the structures with lwstr < RMSD < upstr is counted
RefInfo needs to be prepared to determine RMSD
inscnd : (deprecated) geometrical condition of the solute configuration
0 (default) : random (insorigin = 0, insposition = 0)
1 : spherical (insorigin = 2, insposition = 2)
2 : symmetric bilayer (insorigin = 2, insposition = 4)
3 : reference (insorigin = 3, insposition = 5)
inscfg : (deprecated) position and orientation for the inserted solute
0 (default) : only the intramolecular configuration is from the file
(insorient = 0)
1 : orientation is fixed from the file with random position (insorient = 1)
2 : position and orientation are also fixed from the file
(insorient = 1, insposition = 1)
lwreg : lower bound of the region of solute position
upreg : upper bound of the region of solute position
lwreg and upreg are effective only when insorigin = 2 or 3 and insposition >= 2
lwstr : lower bound of order parameter of solute intramolecular structure
upstr : upper bound of order parameter of solute intramolecular structure
lwstr and upstr are effective only when insstructure = 1
ljformat : input-file format for the LJ energy and length parameters
0 : epsilon (kcal/mol) and sigma (A)
where epsilon and sigma refer to those in the standard expression
of LJ potential of 4 * epsilon * [(sigma / r)**12 - (sigma / r)**6]
1 (default) : 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)
5 : Read from table, LJTable file (epsilon in kcal/mol and sigma in A)
A separate file of LJTable needs to be prepared as described below.
ljswitch : switching function for smooth LJ truncation
0 (default) : potential switch in CHARMM form
1 : potential switch in GROMACS form
2 : force switch in CHARMM form
3 : force switch in GROMACS form (effective as of ver 0.3.2)
tapering function is defined by lwljcut and upljcut variables
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 3 : PPPM
The (full) Ewald is not supported any more, and so cltype = 1 is not active
PPPM is available as of ver 0.3.2
screen : screening parameter in Ewald, PME or PPPM
ewtoler : tolerance in Ewald, PME or PPPM to set the screening parameter
When screen is given, screen has the priority
splodr : order of spline function used in PME or PPPM
ms1max,ms2max,ms3max : number of meshes in PME or PPPM along one direction
inptemp : temperature of the system in Kelvin
temp : temperature of the system in kcal/mol
block_threshold : box size for cell-link list based method in realcal.F90
force_calculation : if set to .true., the program continues to run even if there is a warning
iseed : Random number seed. It determines where and how the solute
is inserted in the reference-solvent system.
If iseed = 0, the seed is initialized based on the 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 : "margin" is added in low energy by shifting ecdmin and ecfmns by finfac*ecfbin pecore : number of discretization in the core interaction region (excluded-volume region)
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 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
ecprread : whether the energy parameters are read from a separate file
0 (default) : user-defined parameters are not read from outside
1 : parameters are read separately from a file EcdInfo
meshread : whether the energy meshes are taken from a separate file
0 (default) : user-defined meshes are not taken from outside
1 : energy coordinate meshes are read from a file EcdMesh
as of ver 0.3.5 and
peread : determines whether the parameters are read from a separate file
0 (default) : parameters are read from parameters_er
1 : parameters are read separately from a file EcdInfo
when the version is 0.3.4 or earlier.
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.
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.
The description concerning the LJ parameters are valid only when the ljformat parameter in parameters_er is <= 4.
When ljformat = 5 in parameters_er, a separate file of LJTable needs to be prepared; see LJTable below.
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; 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
(Version <=0.3)
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 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.
(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
3 C -0.115 7.00E-02 3.5500532 0.268 -0.215 -18.094
…
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 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.
LJTable
The LJTable file contains the LJ parameters between each pair of atoms.
This file is necessarily prepared only when ljformat = 5 in parameters_er.
When ljformat <= 4, only the MolPrmX and SltInfo files need to be prepared in the format described above.
When ljformat = 5, the format of MolPrmX and SltInfo is different from the one described above and reads
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: 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
7
3.06647E+00 0.00000E+00 3.23307E+00 2.76891E+00 2.85800E+00 3.10861E+00 0.00000E+00
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
3.23307E+00 0.00000E+00 3.39967E+00 2.93551E+00 3.02460E+00 3.27521E+00 0.00000E+00
..........
2.10400E-01 0.00000E+00 1.51716E-01 5.74742E-02 5.74742E-02 1.78832E-01 0.00000E+00
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
1.51716E-01 0.00000E+00 1.09400E-01 4.14437E-02 4.14437E-02 1.28953E-01 0.00000E+00
..........
The first line identifies the number of LJ interaction types.
This is the maximum value of the LJ interaction type of each atom specified at the 4th column of MolPrmX or SltInfo.
In the above example, the number of LJ interaction types is 7.
When n is the number of LJ interaction types, the next n lines provides the values of LJ sigma between each pair of LJ interaction types:
sigma(1,1), sigma(1,2), ... sigma(1,n)
sigma(2,1), sigma(2,2), ... sigma(2,n)
..........
sigma(n,1), sigma(n,2), ... sigma(n,n)
After the list of sigma values, epsilon values follow over the next n lines:
epsilon(1,1), epsilon(1,2), ... epsilon(1,n)
epsilon(2,1), epsilon(2,2), ... epsilon(2,n)
..........
epsilon(n,1), epsilon(n,2), ... epsilon(n,n)
In LJTable, the LJ sigma and epsilon are expressed in kcal/mol and A and refer to those in the standard expression of LJ potential of 4 * epsilon * ((sigma / r)^^12 - (sigma / r)^^6)
As noted above with respect to cmbrule, the LJ sigma of unlike atoms is combined either as arithmetic or geometric mean, depending on the cmbrule value; the LJ epsilon is always combined with geometric mean.
Any other form of combination rule is not possible when ljformat <= 4.
When ljformat = 5 is set in parameters_er and the LJTable is prepared, on the other hand,
any values of epsilon and sigma can be assigned to any pair of atoms.
There needs no assumption of combination rule.
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
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.
When the energy parameters are specified in EcdInfo, they have higher proiries than those in the hist section of parameters_er, though the priority is the highest for the coordinate meshes from EcdMesh described below.
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.
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
0 100
0 1 -5.00
0 2 -4.90
..........
0 99 4.80
0 100 5.00
1 1200 200
1 1 -20.00
1 2 -19.95
..........
1 1199 0.9454589E+11
1 1200 0.1000000E+12
..........
3 1550 300
3 1 -25.50
3 2 -25.40
..........
3 1549 4.8500E+11
3 1550 5.0000E+11
with the convention that the energy is expressed in kcal/mol.
When the definitions of energy-coordinate bins are provided in EcdMesh, they have higher proiries than those in the hist section of parameters_er and in EcdInfo described above.
The first column of each line refers to the species; 0 is for the self-energy of the solute and 1, 2, ... is for the solvent species.
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 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, 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)
For those species which are absent in EcdMesh, the binning parameters are taken from parameters_er or EcdInfo.
PermIndex
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
2 2
3 3
4 11
5 12
6 13
...
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 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 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 erdst.
If user has 500 H2O and 100 ETOH molecules,
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 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,
PermIndex needs to be prepared.
Consider, as a very simplified example, a solvent that consists of two CH3-CH2-CH3 molecules.
To treat CH3 and CH2 as distinct solvent species, PermIndex can read
1 1 ! C of the first CH3 in the first molecule
2 2 ! H of the first CH3 in the first molecule
3 3 ! H of the first CH3 in the first molecule
4 4 ! H of the first CH3 in the first molecule
5 17 ! C of the CH2 in the first molecule
6 18 ! H of the CH2 in the first molecule
7 19 ! H of the CH2 in the first molecule
8 5 ! C of the second CH3 in the first molecule
9 6 ! H of the second CH3 in the first molecule
10 7 ! H of the second CH3 in the first molecule
11 8 ! H of the second CH3 in the first molecule
12 9 ! C of the first CH3 in the second molecule
13 10 ! H of the first CH3 in the second molecule
14 11 ! H of the first CH3 in the second molecule
15 12 ! H of the first CH3 in the second molecule
16 20 ! C of the CH2 in the second molecule
17 21 ! H of the CH2 in the second molecule
18 22 ! H of the CH2 in the second molecule
19 13 ! C of the second CH3 of the second molecule
20 14 ! H of the second CH3 of the second molecule
21 15 ! H of the second CH3 of the second molecule
22 16 ! H of the second CH3 of the second molecule
In this case, MDinfo and MolPrmX need to be (manually) modified respectively as
(Number of frames) 2
4 2
4 3
1 C charge on C in CH3 LJ ¥epsilon of C in CH3 LJ ¥sigma of C in CH3
2 H charge on H in CH3 LJ ¥epsilon of H in CH3 LJ ¥sigma of H in CH3
3 H charge on H in CH3 LJ ¥epsilon of H in CH3 LJ ¥sigma of H in CH3
4 H charge on H in CH3 LJ ¥epsilon of H in CH3 LJ ¥sigma of H in CH3
1 C charge on C in CH2 LJ ¥epsilon of C in CH2 LJ ¥sigma of C in CH2
2 H charge on H in CH2 LJ ¥epsilon of H in CH2 LJ ¥sigma of H in CH2
3 H charge on H in CH2 LJ ¥epsilon of H in CH2 LJ ¥sigma of H in CH2
where the above MDinfo is for the reference solvent and the latter two are MolPrm1 for CH3 and MolPrm2 for CH2.
In the (modified) MDinfo, the first and second columns in the second and third lines carry information for CH3 and CH2, respectively.
It is also possible to modify MDinfo and MolPrmX by first changing the topology file for the purpose of introducing the segments and then running gen_structure;
this scheme may be useful since the chemical structures are more evident in the topology files.
Note that only the partial charges and Lennard-Jones parameters are necessary to prepare MolPrmX.
Related
Wiki: FixedLigandBind
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