dcm (c49b1)
Distributed Charge Model (DCM)
By Mike Devereux, Oliver Unke, Eric Boittier,
Markus Meuwly
(Michael.Devereux@unibas.ch, m.meuwly@unibas.ch )
The DCM command allows the use of Distributed Charge Models to compute
the electrostatic energy and force. The method is documented in the
articles 'A Novel, Computationally Efficient Multipolar Model
Employing Distributed Charges for Molecular Dynamics Simulations'
(J. Chem. Theory Comput., 2014, 10, pp
4229-4241. http://dx.doi.org/10.1021/ct500511t) and 'Minimal
distributed charges: Multipolar quality at the cost of point charge
electrostatics.' (J. Chem. Phys. 2017, 147, pp 161712;
https://doi.org/10.1063/1.4993424) If called, the DCM module zeroes
all atomic charges in the standard CHARMM charge arrays, copies their
original values to the DCM routine, adds any off-center DCM charges
for residues that are listed in the specified .dcm parameter file, and
then handles all electrostatics internally. The electrostatic term in
the output file arises purely from the DCM module.
A recent extension implements conformational-dependence of charge
positions via the "FLUX" keyword. Accuracy in electrostatics is
thereby maintained across different conformers
(https://arxiv.org/abs/2206.15366#)
* Syntax | Syntax of DCM Commands
* Description | Description of DCM Commands
* Requirements | Requirements to run DCM calculations
* Capabilities | Description of capabilities
* DCM format | Description of the .dcm topology file
* Examples | Input Files for various examples
By Mike Devereux, Oliver Unke, Eric Boittier,
Markus Meuwly
(Michael.Devereux@unibas.ch, m.meuwly@unibas.ch )
The DCM command allows the use of Distributed Charge Models to compute
the electrostatic energy and force. The method is documented in the
articles 'A Novel, Computationally Efficient Multipolar Model
Employing Distributed Charges for Molecular Dynamics Simulations'
(J. Chem. Theory Comput., 2014, 10, pp
4229-4241. http://dx.doi.org/10.1021/ct500511t) and 'Minimal
distributed charges: Multipolar quality at the cost of point charge
electrostatics.' (J. Chem. Phys. 2017, 147, pp 161712;
https://doi.org/10.1063/1.4993424) If called, the DCM module zeroes
all atomic charges in the standard CHARMM charge arrays, copies their
original values to the DCM routine, adds any off-center DCM charges
for residues that are listed in the specified .dcm parameter file, and
then handles all electrostatics internally. The electrostatic term in
the output file arises purely from the DCM module.
A recent extension implements conformational-dependence of charge
positions via the "FLUX" keyword. Accuracy in electrostatics is
thereby maintained across different conformers
(https://arxiv.org/abs/2206.15366#)
* Syntax | Syntax of DCM Commands
* Description | Description of DCM Commands
* Requirements | Requirements to run DCM calculations
* Capabilities | Description of capabilities
* DCM format | Description of the .dcm topology file
* Examples | Input Files for various examples
Top
Syntax of DCM Commands
[Syntax DCM]
DCM { IUDCm elec-opt-spec [ XYZ IUXYZ ] [ MUL IUMUL ] [ LAMBda real ] }
{ [ FLUX ] }
DCM { S1 IUS1 }
elec-opt-spec::= [ SWITCH ] [ SHIFT ] [ FSHIFT ] [ TSWITCH ] [ TSHIFT ]
Syntax of DCM Commands
[Syntax DCM]
DCM { IUDCm elec-opt-spec [ XYZ IUXYZ ] [ MUL IUMUL ] [ LAMBda real ] }
{ [ FLUX ] }
DCM { S1 IUS1 }
elec-opt-spec::= [ SWITCH ] [ SHIFT ] [ FSHIFT ] [ TSWITCH ] [ TSHIFT ]
Top
Keyword Default Purpose
IUDCm - Fortran unit of .dcm parameter file
(should be opened in input file before using)
LAMBda - Scaling factor to be applied to DCM energy for each energy
evaluation. This option is used for evaluating free energy
contributions in line with the approach of Bereau et al. (Bereau, T.,
Kramer, C., Meuwly, M., J.Chem.Theor.Comput., 2013, 9, 5450-5459)
XYZ - Write Cartesian coordinates of all DCM charges along with
nuclear coordinates to a file for diagnostic purposes or for use in
QM/MM calculations
IUXYZ - Fortran unit of file where all coordinates and charges should
be dumped at every timestep
MUL - Calculate and write atomic multipoles from DCM charge
arrangements of each atom in global reference axis system in GDMA's
'.lpun' format (diagnostic)
IUMUL - Fortran unit of file where total atomic multipole moments
should be dumped
S1 - For thermodynamic integration calculations in
combination with CHARMM's "PERT" keyword only. Defines the "Lambda=1"
product electrostatic state, note that this keyword assumes that the
"Lambda=0" or "initial" TI electrostatic state has already been
defined and stores all existing DCM charges before the "S1" option is
called in a separate array. See test case.
IUS1 - Fortran unit of .dcm parameter file containing DCM charges for
final (product) state
FLUX - Requests activation of conformationally dependent charge positions.
necessary parameters will be read from the IUDCm unit.
Electrostatic cutoff options:
The standard SWITCH, SHIFT and FSHIFT cutoffs have been implemented
but need to be declared separately in the DCM section, overriding
whatever was requested by NBOND. The cutoff values (inner and outer
cutoff, nonbond list cutoff and image cutoff) will be taken from the
NBOND section of the standard CHARMM input file, so only the desired
method needs to be declared in the DCM section.
Note that "SHIFT", "FSHIFT" and "SWITCH" cutoffs have been implemented
such that all DCM charges belonging to the same atom experience the
same damping (the charge-charge distance evaluated is actually the
nucleus-nucleus distance). This can be important for true DCM models
derived directly from multipole expansions, but is not appropriate for
(f)MDCM, TIP4P or TIP5P, where charges are further from the nucleus
and the models were fitted by damping based on the true charge-charge
separation, rather than the nucleus-nucleus separation. For such
models TSHIFT (recommended) or TFSHIFT can be used.
SWITCH - "SWITched" cutoffs will be used, nuclear coordinates are
used to approximate charge-charge distance. See Nbonds.
SHIFT - "SHIFted" cutoffs will be used, nuclear coordinates are used
to approximate charge-charge distance. See Nbonds.
FSHIFT - "FSHIfted" cutoffs will be used, nuclear coordinates are
used to approximate charge-charge distance. See Nbonds.
TFSHIFT - "FSHIFTed" electrostatic cutoffs will be used, charge-charge
distances are used to evaluate cutoffs. See Nbonds.
TSHIFT - Recommended. CHARMM "SHIFted" electrostatic cutoffs will be
used, charge-charge distances are used to evaluate cutoffs. See
Nbonds.
Keyword Default Purpose
IUDCm - Fortran unit of .dcm parameter file
(should be opened in input file before using)
LAMBda - Scaling factor to be applied to DCM energy for each energy
evaluation. This option is used for evaluating free energy
contributions in line with the approach of Bereau et al. (Bereau, T.,
Kramer, C., Meuwly, M., J.Chem.Theor.Comput., 2013, 9, 5450-5459)
XYZ - Write Cartesian coordinates of all DCM charges along with
nuclear coordinates to a file for diagnostic purposes or for use in
QM/MM calculations
IUXYZ - Fortran unit of file where all coordinates and charges should
be dumped at every timestep
MUL - Calculate and write atomic multipoles from DCM charge
arrangements of each atom in global reference axis system in GDMA's
'.lpun' format (diagnostic)
IUMUL - Fortran unit of file where total atomic multipole moments
should be dumped
S1 - For thermodynamic integration calculations in
combination with CHARMM's "PERT" keyword only. Defines the "Lambda=1"
product electrostatic state, note that this keyword assumes that the
"Lambda=0" or "initial" TI electrostatic state has already been
defined and stores all existing DCM charges before the "S1" option is
called in a separate array. See test case.
IUS1 - Fortran unit of .dcm parameter file containing DCM charges for
final (product) state
FLUX - Requests activation of conformationally dependent charge positions.
necessary parameters will be read from the IUDCm unit.
Electrostatic cutoff options:
The standard SWITCH, SHIFT and FSHIFT cutoffs have been implemented
but need to be declared separately in the DCM section, overriding
whatever was requested by NBOND. The cutoff values (inner and outer
cutoff, nonbond list cutoff and image cutoff) will be taken from the
NBOND section of the standard CHARMM input file, so only the desired
method needs to be declared in the DCM section.
Note that "SHIFT", "FSHIFT" and "SWITCH" cutoffs have been implemented
such that all DCM charges belonging to the same atom experience the
same damping (the charge-charge distance evaluated is actually the
nucleus-nucleus distance). This can be important for true DCM models
derived directly from multipole expansions, but is not appropriate for
(f)MDCM, TIP4P or TIP5P, where charges are further from the nucleus
and the models were fitted by damping based on the true charge-charge
separation, rather than the nucleus-nucleus separation. For such
models TSHIFT (recommended) or TFSHIFT can be used.
SWITCH - "SWITched" cutoffs will be used, nuclear coordinates are
used to approximate charge-charge distance. See Nbonds.
SHIFT - "SHIFted" cutoffs will be used, nuclear coordinates are used
to approximate charge-charge distance. See Nbonds.
FSHIFT - "FSHIfted" cutoffs will be used, nuclear coordinates are
used to approximate charge-charge distance. See Nbonds.
TFSHIFT - "FSHIFTed" electrostatic cutoffs will be used, charge-charge
distances are used to evaluate cutoffs. See Nbonds.
TSHIFT - Recommended. CHARMM "SHIFted" electrostatic cutoffs will be
used, charge-charge distances are used to evaluate cutoffs. See
Nbonds.
Top
Requirements
A DCM calculation requires a 'DCM' section in the CHARMM input file
and an external file (typically with extension '.dcm') containing the
DCM charges for each DCM residue.
The calculation proceeds by first setting up the simulation, defining
atom types, force field parameters, sequence, atomic coordinates
etc. as usual. Periodic boundaries and nonbonded cutoffs can also be
configured before calling DCM. Once simulation setup is otherwise
complete a call is made in the input file to the DCM module to add DCM
charges to all atoms with a residue type mentioned in the .dcm
parameter file. A call to 'ENERgy' before and after calling 'DCM' in
the CHARMM input file should reveal a change in the electrostatic
interaction energy after DCM initialization. After initializing the
DCM module it will be called each time the energy is updated.
If DCM is to be used in conjunction with CHARMM's "PERT" module for
thermodynamic integration, then the initial lambda=0 state should be
set up before calling DCM with the corresponding lambda=0 .dcm
parameter file, and then "PERT" to store the initial state. The system
should then be modified as appropriate to form the lambda=1 final
state and the DCM command should be called again with the "S1" option
to read in a second "lambda=1" .dcm parameter file prepared by the
user to define the final state. Dynamics for the given TI window can
then begin. See test case.
In order to use conformationally-dependent charges with the "FLUX"
keyword, the necessary parameters must be added to the .dcm parameter
file.
Requirements
A DCM calculation requires a 'DCM' section in the CHARMM input file
and an external file (typically with extension '.dcm') containing the
DCM charges for each DCM residue.
The calculation proceeds by first setting up the simulation, defining
atom types, force field parameters, sequence, atomic coordinates
etc. as usual. Periodic boundaries and nonbonded cutoffs can also be
configured before calling DCM. Once simulation setup is otherwise
complete a call is made in the input file to the DCM module to add DCM
charges to all atoms with a residue type mentioned in the .dcm
parameter file. A call to 'ENERgy' before and after calling 'DCM' in
the CHARMM input file should reveal a change in the electrostatic
interaction energy after DCM initialization. After initializing the
DCM module it will be called each time the energy is updated.
If DCM is to be used in conjunction with CHARMM's "PERT" module for
thermodynamic integration, then the initial lambda=0 state should be
set up before calling DCM with the corresponding lambda=0 .dcm
parameter file, and then "PERT" to store the initial state. The system
should then be modified as appropriate to form the lambda=1 final
state and the DCM command should be called again with the "S1" option
to read in a second "lambda=1" .dcm parameter file prepared by the
user to define the final state. Dynamics for the given TI window can
then begin. See test case.
In order to use conformationally-dependent charges with the "FLUX"
keyword, the necessary parameters must be added to the .dcm parameter
file.
Top
Capabilities
The DCM code has been integrated with standard CHARMM machinery for
periodic boundaries, non-bonded cutoffs, constant-pressure
simulations and Ewald summation.
There is no requirement for all moieties in a system to carry DCM
charges, akin to QM/MM simulations. A standard CHARMM simulation can
be set up with only certain residues of interest assigned DCM charges,
any atom-centered charges will be passed to the DCM module and the
split-level atom-centered/DCM simulation will proceed automatically.
The DCM charges and Cartesian coordinates can be dumped to a file at
every timestep using the 'XYZ' command in the DCM block of the input
file. This file can be used diagnostically or parsed and used to pass
the DCM charges as external point charges in a QM/MM calculation. It
is not yet implemented to specify how frequently this file should be
updated, or to specify a subgroup of the atoms to be dumped.
The code works for diatomics as long as all DCM charges lie along the
bond axis, as the bond is used to define the z-axis while the x- and
y-axes remain undefined.
Free Energy Calculations have been implemented using CHARMM's PERT
routines. To use this feature, add a standard DCM section before the
PERT command is called that reads a .dcm parameter file for the
LAMBDA=0 state. Call PERT as usual for a standard CHARMM TI run. After
PERT you should define your LAMBDA=1 state by calling the DCM routine
again, but this time read in a second .dcm file with the keyword 'S1'
A simple polarization routine is included in the DCM module, where an
isotropic polarizability can be assigned to each atom in the dcm
charge parameter file. To maintain computational efficiency a
single-iteration approximation is used, i.e. rather than the induced
dipole on an atom modifying the electric field of other atoms and
inducing a new dipole, iterating until self-consistency, we stop after
a single iteration. This is equivalent to assuming that induced
dipoles are caused only by the permanent electric field of surrounding
moieties, and are not affected by the surrounding induced dipoles. As
such, the polarizability should be treated as a parameter to be
fitted, rather than a physically measurable quantity. The damping
function employed in the AMOEBA force field (J Phys Chem B. 2010
March 4; 114(8): 2549–2564. doi:10.1021/jp910674d ) is used here.
The maximum number of charge sites per atom is 7, as typically no more
than 1-3 charges per atom are required.
PSF FILES
Note: the routine does not add DCM charges to the standard CHARMM PSF
file, and central charges are zeroed. This means that you cannot save
and load DCM charges from a PSF file, and you cannot save non-DCM
charges to the PSF after calling the DCM routine. The system must
instead be reinitialized, add charges from the topology and .dcm
files as before.
SHAKE
Use of SHAKE is supported, but is not yet compatible with the "FAST
WATER" option. Use instead the older (and more general) "SHAKE BOND"
approach.
FLEXIBLE CHARGE MODELS (fMDCM)
This feature is developmental and currently only allows coupling of
charge positions to specified angular degrees of freedom. Extension to
allow coupling to arbitrary degrees of freedom is in progress. A
sample parameter file is provided with the corresponding test case.
Capabilities
The DCM code has been integrated with standard CHARMM machinery for
periodic boundaries, non-bonded cutoffs, constant-pressure
simulations and Ewald summation.
There is no requirement for all moieties in a system to carry DCM
charges, akin to QM/MM simulations. A standard CHARMM simulation can
be set up with only certain residues of interest assigned DCM charges,
any atom-centered charges will be passed to the DCM module and the
split-level atom-centered/DCM simulation will proceed automatically.
The DCM charges and Cartesian coordinates can be dumped to a file at
every timestep using the 'XYZ' command in the DCM block of the input
file. This file can be used diagnostically or parsed and used to pass
the DCM charges as external point charges in a QM/MM calculation. It
is not yet implemented to specify how frequently this file should be
updated, or to specify a subgroup of the atoms to be dumped.
The code works for diatomics as long as all DCM charges lie along the
bond axis, as the bond is used to define the z-axis while the x- and
y-axes remain undefined.
Free Energy Calculations have been implemented using CHARMM's PERT
routines. To use this feature, add a standard DCM section before the
PERT command is called that reads a .dcm parameter file for the
LAMBDA=0 state. Call PERT as usual for a standard CHARMM TI run. After
PERT you should define your LAMBDA=1 state by calling the DCM routine
again, but this time read in a second .dcm file with the keyword 'S1'
A simple polarization routine is included in the DCM module, where an
isotropic polarizability can be assigned to each atom in the dcm
charge parameter file. To maintain computational efficiency a
single-iteration approximation is used, i.e. rather than the induced
dipole on an atom modifying the electric field of other atoms and
inducing a new dipole, iterating until self-consistency, we stop after
a single iteration. This is equivalent to assuming that induced
dipoles are caused only by the permanent electric field of surrounding
moieties, and are not affected by the surrounding induced dipoles. As
such, the polarizability should be treated as a parameter to be
fitted, rather than a physically measurable quantity. The damping
function employed in the AMOEBA force field (J Phys Chem B. 2010
March 4; 114(8): 2549–2564. doi:10.1021/jp910674d ) is used here.
The maximum number of charge sites per atom is 7, as typically no more
than 1-3 charges per atom are required.
PSF FILES
Note: the routine does not add DCM charges to the standard CHARMM PSF
file, and central charges are zeroed. This means that you cannot save
and load DCM charges from a PSF file, and you cannot save non-DCM
charges to the PSF after calling the DCM routine. The system must
instead be reinitialized, add charges from the topology and .dcm
files as before.
SHAKE
Use of SHAKE is supported, but is not yet compatible with the "FAST
WATER" option. Use instead the older (and more general) "SHAKE BOND"
approach.
FLEXIBLE CHARGE MODELS (fMDCM)
This feature is developmental and currently only allows coupling of
charge positions to specified angular degrees of freedom. Extension to
allow coupling to arbitrary degrees of freedom is in progress. A
sample parameter file is provided with the corresponding test case.
Top
DCM file format
The DCM parameter file (extension .dcm ) will load the following
information / parameters:
NR NFX: The number of residue types with DCM charges and
polarizabilities (for a solute in solvent NR=2) and the number of
residue types with flexible charges)
NAME: The name of the residue as in the psf file.
NFRAMES: The total number of axis system frames required for the
residue, see J. Chem. Theory Comput., 2014, 10 (10), pp 4229–4241 for
a description of the local axis system and how to define them.
Na Nb Nc SAXIS: Atom indices to define the axis system frames and the
type of axis system to use for atoms Na, Nb, Nc. SAXIS is the type of
axis system. Two keywords exist BO and BI corresponding to bond or
bisector z-axis. BO will use atom a and b to define the local z axis,
BI uses the bisector of a b c. Note that in the line 'Na Nb Nc', if
the third atom index Nc is set to '0' the molecule is taken to be a
diatomic and only two atoms (i.e. information for atoms a and b) are
expected to follow.
NCa NPa: the number of charges and polarizable sites for atom a
POSX POSY POSZ CV: x, y, z positions of the charge sites with the atom
at (0 0 0) and the magnitude of the charge
PVa: value of isotropic polarizability for atom a
NOTES:
Identical blocks follow for atoms b and c. If an atom index occurs in
multiple frames only one such block is given and in all other frames
the number of charges and polarizable sites is set to "0 0", see
examples below.
For each axis system frame defined in a DCM parameter file, three
local axis systems (one for each atom) are constructed with the
origins taken at the position of each atomic nucleus. The number of
charges and polarizable sites per atom (local axis system) and the
position (in Angstrom) of each charge in its local axis system are
also defined, along with the corresponding values of charges and
polarizabilities (optional) in (a.u).
To summarize, once an axis system frame for atoms a,b,c is defined,
the number, (x,y,z)-position and magnitude of charges (and polarizable
sites if requested) for atom a in its local axis system, then for atom
b and then the same for atom c are defined next.
The .dcm file has a fixed format, see examples.
If an atom appears in more than one axis system frame, then in the
.dcm file, the number of charges and charge values for this same atom
have to be declared multiple times, but the charges will be non zero
in only one axis system frame. See also the explanation in the first
paragraph, page 4232 of J. Chem. Theory Comput., 2014, 10 (10), pp
4229–4241 . See example below.
DCM file format
The DCM parameter file (extension .dcm ) will load the following
information / parameters:
NR NFX: The number of residue types with DCM charges and
polarizabilities (for a solute in solvent NR=2) and the number of
residue types with flexible charges)
NAME: The name of the residue as in the psf file.
NFRAMES: The total number of axis system frames required for the
residue, see J. Chem. Theory Comput., 2014, 10 (10), pp 4229–4241 for
a description of the local axis system and how to define them.
Na Nb Nc SAXIS: Atom indices to define the axis system frames and the
type of axis system to use for atoms Na, Nb, Nc. SAXIS is the type of
axis system. Two keywords exist BO and BI corresponding to bond or
bisector z-axis. BO will use atom a and b to define the local z axis,
BI uses the bisector of a b c. Note that in the line 'Na Nb Nc', if
the third atom index Nc is set to '0' the molecule is taken to be a
diatomic and only two atoms (i.e. information for atoms a and b) are
expected to follow.
NCa NPa: the number of charges and polarizable sites for atom a
POSX POSY POSZ CV: x, y, z positions of the charge sites with the atom
at (0 0 0) and the magnitude of the charge
PVa: value of isotropic polarizability for atom a
NOTES:
Identical blocks follow for atoms b and c. If an atom index occurs in
multiple frames only one such block is given and in all other frames
the number of charges and polarizable sites is set to "0 0", see
examples below.
For each axis system frame defined in a DCM parameter file, three
local axis systems (one for each atom) are constructed with the
origins taken at the position of each atomic nucleus. The number of
charges and polarizable sites per atom (local axis system) and the
position (in Angstrom) of each charge in its local axis system are
also defined, along with the corresponding values of charges and
polarizabilities (optional) in (a.u).
To summarize, once an axis system frame for atoms a,b,c is defined,
the number, (x,y,z)-position and magnitude of charges (and polarizable
sites if requested) for atom a in its local axis system, then for atom
b and then the same for atom c are defined next.
The .dcm file has a fixed format, see examples.
If an atom appears in more than one axis system frame, then in the
.dcm file, the number of charges and charge values for this same atom
have to be declared multiple times, but the charges will be non zero
in only one axis system frame. See also the explanation in the first
paragraph, page 4232 of J. Chem. Theory Comput., 2014, 10 (10), pp
4229–4241 . See example below.
Top
Examples
!----------------------------------EXAMPLE H2O--------------------------------!
The following is a .dcm file for water, which provides a simple example as
there is only one frame and two off-center charges per atom. All atoms are
non-polarizable.
!-----------Next line is begining of the .dcm file for H2O--------------------!
1 0 ! no. residue types defined here (DCM and fMDCM)
WAT ! residue name
1 ! no. axis system frames
2 1 3 BI ! atom indices involved in frame 1
2 0 ! no. chgs and polarizable sites for atom 2
0.1260132091 0.0000000000 -0.4814804450 -0.5276865387
0.0866301185 0.0000000000 -0.1171477518 0.7043758247
2 0 ! no. chgs and polarizable sites for atom 1
0.0000000000 -0.5064709322 -0.0140790018 -0.1766892860
-0.0000000000 0.5064709322 -0.0140790018 -0.1766892860
2 0 ! no. chgs and polarizable sites for atom 3
-0.1260132091 0.0000000000 -0.4814804450 -0.5276865387
-0.0866301185 0.0000000000 -0.1171477518 0.7043758247
! Note that in the line '2 1 3 BI', if the third atom index is set to
! '0' the molecule is taken to be a diatomic and only two atoms (with
! up to 7 DCM charges each) are expected to follow.
!-----------------------end of the .dcm file for H2O--------------------------!
!----------------Example .dcm file for benzene and water--------!
2 0 ! Number of residue types defined here (DCM and fMDCM)
BENZ ! Residue name (matches topology file)
6 ! Number of axis system frames
7 1 2 BO ! atom indices involved in frame 1 (C-atoms are 1-6)
2 0 ! no. chgs and polarizable sites for atom 7
0.0000237914 0.0000035914 0.3999765788 0.2157846427
0.0000220194 0.0000033239 0.3701860224 -0.1759614527
3 0 ! no. chgs and polarizable sites for atom 1
0.0000053592 0.0000008090 0.0900970650 0.9997069079
0.0000081055 0.3677817712 0.1054518383 -0.5197650489
-0.0000514046 -0.3677661170 0.1054584463 -0.5197650489
3 0 ! no. chgs and polarizable sites for atom 2
0.0780263518 0.0000008090 0.0450501592 0.9997069079
0.0913230600 0.3677817712 0.0527291321 -0.5197650489
0.0913585348 -0.3677661170 0.0526808967 -0.5197650489
8 2 3 BO ! atom indices involved in frame 1
2 0 ! no. chgs and polarizable sites for atom 8
-0.0000517033 -0.0000963053 0.3999737720 0.2157846427
-0.0000494046 -0.0000945870 0.3701832157 -0.1759614527
0 0 ! no. chgs and polarizable sites for atom 2
3 0 ! no. chgs and polarizable sites for atom 3
0.0780273314 -0.0000051967 0.0450437115 0.9997069079
0.0913526674 0.3677747410 0.0527221302 -0.5197650489
0.0913315263 -0.3677731478 0.0526738921 -0.5197650489
9 3 4 BO ! atom indices involved in frame 1
2 0 ! no. chgs and polarizable sites for atom 9
0.0002666349 -0.0000001328 0.3999753458 0.2157846427
0.0002626520 -0.0000003264 0.3701847896 -0.1759614527
0 0 ! no. chgs and polarizable sites for atom 3
3 0 ! no. chgs and polarizable sites for atom 4
0.0780259161 0.0000005853 0.0450485706 0.9997069079
0.0913330536 0.3677815091 0.0527113051 -0.5197650489
0.0913476264 -0.3677663813 0.0526956220 -0.5197650489
10 4 5 BO ! atom indices involved in frame 1
2 0 ! no. chgs and polarizable sites for atom 10
-0.0000732361 -0.0000550881 0.3999765184 0.2157846427
-0.0000704813 -0.0000541892 0.3701859621 -0.1759614527
0 0 ! no. chgs and polarizable sites for atom 4
3 0 ! no. chgs and polarizable sites for atom 5
0.0780284766 -0.0000027185 0.0450454039 0.9997069079
0.0913493160 0.3677776417 0.0527113771 -0.5197650489
0.0913371415 -0.3677702485 0.0526880754 -0.5197650489
11 5 6 BO ! atom indices involved in frame 1
2 0 ! no. chgs and polarizable sites for atom 11
0.0002288551 -0.0000009386 0.3999730724 0.2157846427
0.0002256085 -0.0000011161 0.3701825162 -0.1759614527
0 0 ! no. chgs and polarizable sites for atom 5
3 0 ! no. chgs and polarizable sites for atom 6
0.0780236157 0.0000005367 0.0450500425 0.9997069079
0.0913175370 0.3677814524 0.0527360645 -0.5197650489
0.0913586037 -0.3677664345 0.0526736993 -0.5197650489
12 6 1 BO ! atom indices involved in frame 1
2 0 ! no. chgs and polarizable sites for atom 12
-0.0000170811 -0.0000068707 0.3999746473 0.2157846427
-0.0000154980 -0.0000069303 0.3701840909 -0.1759614527
0 0 ! no. chgs and polarizable sites for atom 6
0 0 ! no. chgs and polarizable sites for atom 1
WAT ! residue name
1 ! no. axis system frames
2 1 3 BI ! atom indices involved in frame 1
2 0 ! no. chgs and polarizable sites for atom 2
0.1260132091 0.0000000000 -0.4814804450 -0.5276865387
0.0866301185 0.0000000000 -0.1171477518 0.7043758247
2 0 ! no. chgs and polarizable sites for atom 1
0.0000000000 -0.5064709322 -0.0140790018 -0.1766892860
-0.0000000000 0.5064709322 -0.0140790018 -0.1766892860
2 0 ! no. chgs and polarizable sites for atom 3
-0.1260132091 0.0000000000 -0.4814804450 -0.5276865387
-0.0866301185 0.0000000000 -0.1171477518 0.7043758247
!---------------------END of file .dcm---------------------------------------!
Examples
!----------------------------------EXAMPLE H2O--------------------------------!
The following is a .dcm file for water, which provides a simple example as
there is only one frame and two off-center charges per atom. All atoms are
non-polarizable.
!-----------Next line is begining of the .dcm file for H2O--------------------!
1 0 ! no. residue types defined here (DCM and fMDCM)
WAT ! residue name
1 ! no. axis system frames
2 1 3 BI ! atom indices involved in frame 1
2 0 ! no. chgs and polarizable sites for atom 2
0.1260132091 0.0000000000 -0.4814804450 -0.5276865387
0.0866301185 0.0000000000 -0.1171477518 0.7043758247
2 0 ! no. chgs and polarizable sites for atom 1
0.0000000000 -0.5064709322 -0.0140790018 -0.1766892860
-0.0000000000 0.5064709322 -0.0140790018 -0.1766892860
2 0 ! no. chgs and polarizable sites for atom 3
-0.1260132091 0.0000000000 -0.4814804450 -0.5276865387
-0.0866301185 0.0000000000 -0.1171477518 0.7043758247
! Note that in the line '2 1 3 BI', if the third atom index is set to
! '0' the molecule is taken to be a diatomic and only two atoms (with
! up to 7 DCM charges each) are expected to follow.
!-----------------------end of the .dcm file for H2O--------------------------!
!----------------Example .dcm file for benzene and water--------!
2 0 ! Number of residue types defined here (DCM and fMDCM)
BENZ ! Residue name (matches topology file)
6 ! Number of axis system frames
7 1 2 BO ! atom indices involved in frame 1 (C-atoms are 1-6)
2 0 ! no. chgs and polarizable sites for atom 7
0.0000237914 0.0000035914 0.3999765788 0.2157846427
0.0000220194 0.0000033239 0.3701860224 -0.1759614527
3 0 ! no. chgs and polarizable sites for atom 1
0.0000053592 0.0000008090 0.0900970650 0.9997069079
0.0000081055 0.3677817712 0.1054518383 -0.5197650489
-0.0000514046 -0.3677661170 0.1054584463 -0.5197650489
3 0 ! no. chgs and polarizable sites for atom 2
0.0780263518 0.0000008090 0.0450501592 0.9997069079
0.0913230600 0.3677817712 0.0527291321 -0.5197650489
0.0913585348 -0.3677661170 0.0526808967 -0.5197650489
8 2 3 BO ! atom indices involved in frame 1
2 0 ! no. chgs and polarizable sites for atom 8
-0.0000517033 -0.0000963053 0.3999737720 0.2157846427
-0.0000494046 -0.0000945870 0.3701832157 -0.1759614527
0 0 ! no. chgs and polarizable sites for atom 2
3 0 ! no. chgs and polarizable sites for atom 3
0.0780273314 -0.0000051967 0.0450437115 0.9997069079
0.0913526674 0.3677747410 0.0527221302 -0.5197650489
0.0913315263 -0.3677731478 0.0526738921 -0.5197650489
9 3 4 BO ! atom indices involved in frame 1
2 0 ! no. chgs and polarizable sites for atom 9
0.0002666349 -0.0000001328 0.3999753458 0.2157846427
0.0002626520 -0.0000003264 0.3701847896 -0.1759614527
0 0 ! no. chgs and polarizable sites for atom 3
3 0 ! no. chgs and polarizable sites for atom 4
0.0780259161 0.0000005853 0.0450485706 0.9997069079
0.0913330536 0.3677815091 0.0527113051 -0.5197650489
0.0913476264 -0.3677663813 0.0526956220 -0.5197650489
10 4 5 BO ! atom indices involved in frame 1
2 0 ! no. chgs and polarizable sites for atom 10
-0.0000732361 -0.0000550881 0.3999765184 0.2157846427
-0.0000704813 -0.0000541892 0.3701859621 -0.1759614527
0 0 ! no. chgs and polarizable sites for atom 4
3 0 ! no. chgs and polarizable sites for atom 5
0.0780284766 -0.0000027185 0.0450454039 0.9997069079
0.0913493160 0.3677776417 0.0527113771 -0.5197650489
0.0913371415 -0.3677702485 0.0526880754 -0.5197650489
11 5 6 BO ! atom indices involved in frame 1
2 0 ! no. chgs and polarizable sites for atom 11
0.0002288551 -0.0000009386 0.3999730724 0.2157846427
0.0002256085 -0.0000011161 0.3701825162 -0.1759614527
0 0 ! no. chgs and polarizable sites for atom 5
3 0 ! no. chgs and polarizable sites for atom 6
0.0780236157 0.0000005367 0.0450500425 0.9997069079
0.0913175370 0.3677814524 0.0527360645 -0.5197650489
0.0913586037 -0.3677664345 0.0526736993 -0.5197650489
12 6 1 BO ! atom indices involved in frame 1
2 0 ! no. chgs and polarizable sites for atom 12
-0.0000170811 -0.0000068707 0.3999746473 0.2157846427
-0.0000154980 -0.0000069303 0.3701840909 -0.1759614527
0 0 ! no. chgs and polarizable sites for atom 6
0 0 ! no. chgs and polarizable sites for atom 1
WAT ! residue name
1 ! no. axis system frames
2 1 3 BI ! atom indices involved in frame 1
2 0 ! no. chgs and polarizable sites for atom 2
0.1260132091 0.0000000000 -0.4814804450 -0.5276865387
0.0866301185 0.0000000000 -0.1171477518 0.7043758247
2 0 ! no. chgs and polarizable sites for atom 1
0.0000000000 -0.5064709322 -0.0140790018 -0.1766892860
-0.0000000000 0.5064709322 -0.0140790018 -0.1766892860
2 0 ! no. chgs and polarizable sites for atom 3
-0.1260132091 0.0000000000 -0.4814804450 -0.5276865387
-0.0866301185 0.0000000000 -0.1171477518 0.7043758247
!---------------------END of file .dcm---------------------------------------!