- Home
- CHARMM Documentation
- Version c49b1
- extbond

# extbond (c49b1)

External Bond Module *

by

Pierre-Andre Cazade

Marco Pezzella

Debasish Koner

Markus Meuwly

References:

EXTBOND provides additional bond potential forms, besides the usual

harmonic one provided in CHARMM. The module works by substituting the

harmonic potential of a bond defined in the PSF file for a new

potential and is primarily intended but not limited to applications in

spectroscopy. The PSF remains unchanged. EXTBOND can also add new

bonds, which are not present in the PSF file. Those bonds are not

explicitly added to the PSF file and only exist for the duration of a

References:

[1] Oliver T. Unke and Markus Meuwly, J. Chem. Inf. Model., 2017, 57 (8),

pp 1923â€“1931

Syntax :: Syntax of the EXTBOND module.

Description :: A brief description of the module and how it works.

Parameter file (optional) :: Shows how to use the parameter file.

Implemented Kernels :: Reproducing kernels available in the module.

How to build the grid :: Brief description of how to build a grid.

Example :: Description of the example: N-Methylacetamide (NMA).

!--------------------------------Syntax--------------------------------!

XTBD { READ UNIT integer }

{ ADDI { HARM k0 (real) r0 (real) } } double selection

{ { AMOE k0 (real) r0 (real) } }

{ { MORS D0 (real) r0 (real) beta (real) } }

{ { QUAR k0 (real) r0 (real) k1 (real) k2 (real) } }

{ { RKHS filename(char) kerneltype(char) asymptote (char)} }

{ REPL { HARM k0 (real) r0 (real) } } double selection

{ { AMOE k0 (real) r0 (real) } }

{ { MORS D0 (real) r0 (real) beta (real) } }

{ { QUAR k0 (real) r0 (real) k1 (real) k2 (real) } }

{ { RKHS filename (char) kerneltype (char) asymptote (char) } }

{ CLEA }

READ option will identify the additional/replacement bonds in the

specified unit file. Information about the input file will be given in

the next section.

ADDI adds bonds between successive atom pairs between the first and

second selections with the potential of choice.

REPL replaces all existing bonds between the first and second

selections with the potential of choice.

CLEA remove any additional/substituting potential.

HARM for a harmonic potential: k0*(r-r0)**2

AMOE for an MM3 anharmonic bond potential used in AMOEBA

MORS for a Morse potential D0*(1-exp(-beta*(r-r0)))**2

QUAR for the quartic potential : k0*(r-r0)**2+k1*(r-r0)**3+k2*(r-r0)**4

RKHS for Reproducing Kernel Hilbert Space: a grid of n points

of distances and energies.

For RKHS the following information are required:

1- The external file is an ordered set of interatomic distances and

energies, described in the "How to build the grid" section. This file

can be given in the csv format or direct as kernels. Notice that the

filename has to be given without extension. The routine checks for

the existence of a ".kernel" file with the specified name, if does not

exist, it will look for the ".csv" and create the new ".kernel" file.

2- Kerneltype: An integer number that describes the type of kernel to

be used. For available kernel types see the "Implemented Kernels"

section below. For additional technical details see reference [1].

3- Asymptote: A real number that rescales the bond energy to the

correct dissociation energy. Due to the kernels implementiation, the

asympotic energy needs to go to zero.

!--------------------------------Description-------------------------------!

EXTBOND is invoked by the XTBD command. At first the module reads the

parameters for the new bond and the atoms involved. The new bond

definition will be considered only for the present run of CHARMM, no

modifications will be applied to the PSF file.

No modifications are needed in the parameter files.

No compatibility issues with other modules in CHARMM are registered.

!-----------------------------Parameter file-----------------------------!

The bond parameters can be given both: internally in the input file or

externally.

The definition of the bond in the external file is presented here.

The first line is an integer number that defines the number of bonds

present in the external file. The second and third lines define the

bond type and atoms involved with its parameters respectively. In the

next lines a dummy example can be found.

N ! number of bonds defined in the file

TYPE ! typology of bond

ATOM1 ATOM2 parameters ! atoms involved in the new bond and bond parameters.

repeat the second and third line N-1 times.

Example::

!--- CHARMM input file

... parameters defintions....

open unit 40 card name yourdatafile

XTBD read unit 40

... the rest of the input

HARM

1 2 600.00 1.23

AMOE

3 4 600.00 1.23

MORS

5 6 120.0 1.21 2.7

QUAR

7 8 110.0 1.2 50. 20.0

RKHS

9 10 pes 0 K1D -121.9746

!-------------------------Implemented Kernels-------------------------!

For more details see reference [1].

0 -> Reciprocal Power N2 M6 Kernel

1 -> Reciprocal Power N3 M6 Kernel

2 -> Reciprocal Power N2 M5 Kernel

3 -> Reciprocal Power N3 M5 Kernel

4 -> Reciprocal Power N2 M4 Kernel

5 -> Reciprocal Power N3 M4 Kernel

6 -> Reciprocal Power N2 M3 Kernel

7 -> Reciprocal Power N3 M3 Kernel

8 -> Reciprocal Power N2 M2 Kernel

9 -> Reciprocal Power N3 M2 Kernel

10 -> Reciprocal Power N2 M1 Kernel

11 -> Reciprocal Power N3 M1 Kernel

12 -> Reciprocal Power N2 M0 Kernel

13 -> Reciprocal Power N3 M0 Kernel

14 -> Exponetial Decay N2 kernel

15 -> Exponetial Decay N2 kernel

N describes the number of terms used in the Kernels, M describes the

degree of the polynomial expansion.

Reciprocal Power Decay:: Those kernels describe a decay of the form of

1/r^(m+1) decay for values larger than the greatest point in the

grid. The kernel is defined for values on the interval [0,infinity).

Laplacian:: Necessary to evaluate the Laplacian kernel given by

exp(||x-x'||/sigma). Note that sigma can be set to any positive

value, but is initialized automatically with the value 1. It is not

recommended for interpolating potential energy surfaces. The kernel is

only defined on the interval [0,infinity).

Exponential Decay:: For values larger than the greatest point in the

grid, the kernel decays exponentially with exp(-beta*x). Note that

beta can be set to any positive value, but is initialized

automatically with the value 1. This type of kernel is recommended

for short-range intermolecular interactions, which often decay

exponentially. The kernel is only defined for values in the interval

[0,infinity).

For most applications a chemical bond can be described by a Reciprocal

Power N2 M6 Kernel (option "0").

!------------------------- How to build a grid-------------------------!

1) For each bond that should be reproduced by a kernel, perform an Ab

Initio calculation along a scan of the bond.

2) Save the bond length and the energies (in AKMA units), in

increasing order of r in a csv file.

r1 , E1

r2 , E2

....

rN , EN

3) Reference the energies to the asymptote E - E_asympt, such that

E(r_asympt)=0.

!-----------------------------------Example-----------------------------------!

The xtbd_nma.inp test case with the parameter xtbd_nma.para parameter

file and the xtbd_pes.csv, that contains the kernel, are distributed

with the package. This example describes the vibrational analysis and

free dynamics of the NMA molecule with the EXTBOND module invoked for

the C=O bond.

by

Pierre-Andre Cazade

Marco Pezzella

Debasish Koner

Markus Meuwly

References:

EXTBOND provides additional bond potential forms, besides the usual

harmonic one provided in CHARMM. The module works by substituting the

harmonic potential of a bond defined in the PSF file for a new

potential and is primarily intended but not limited to applications in

spectroscopy. The PSF remains unchanged. EXTBOND can also add new

bonds, which are not present in the PSF file. Those bonds are not

explicitly added to the PSF file and only exist for the duration of a

References:

[1] Oliver T. Unke and Markus Meuwly, J. Chem. Inf. Model., 2017, 57 (8),

pp 1923â€“1931

Syntax :: Syntax of the EXTBOND module.

Description :: A brief description of the module and how it works.

Parameter file (optional) :: Shows how to use the parameter file.

Implemented Kernels :: Reproducing kernels available in the module.

How to build the grid :: Brief description of how to build a grid.

Example :: Description of the example: N-Methylacetamide (NMA).

!--------------------------------Syntax--------------------------------!

XTBD { READ UNIT integer }

{ ADDI { HARM k0 (real) r0 (real) } } double selection

{ { AMOE k0 (real) r0 (real) } }

{ { MORS D0 (real) r0 (real) beta (real) } }

{ { QUAR k0 (real) r0 (real) k1 (real) k2 (real) } }

{ { RKHS filename(char) kerneltype(char) asymptote (char)} }

{ REPL { HARM k0 (real) r0 (real) } } double selection

{ { AMOE k0 (real) r0 (real) } }

{ { MORS D0 (real) r0 (real) beta (real) } }

{ { QUAR k0 (real) r0 (real) k1 (real) k2 (real) } }

{ { RKHS filename (char) kerneltype (char) asymptote (char) } }

{ CLEA }

READ option will identify the additional/replacement bonds in the

specified unit file. Information about the input file will be given in

the next section.

ADDI adds bonds between successive atom pairs between the first and

second selections with the potential of choice.

REPL replaces all existing bonds between the first and second

selections with the potential of choice.

CLEA remove any additional/substituting potential.

HARM for a harmonic potential: k0*(r-r0)**2

AMOE for an MM3 anharmonic bond potential used in AMOEBA

MORS for a Morse potential D0*(1-exp(-beta*(r-r0)))**2

QUAR for the quartic potential : k0*(r-r0)**2+k1*(r-r0)**3+k2*(r-r0)**4

RKHS for Reproducing Kernel Hilbert Space: a grid of n points

of distances and energies.

For RKHS the following information are required:

1- The external file is an ordered set of interatomic distances and

energies, described in the "How to build the grid" section. This file

can be given in the csv format or direct as kernels. Notice that the

filename has to be given without extension. The routine checks for

the existence of a ".kernel" file with the specified name, if does not

exist, it will look for the ".csv" and create the new ".kernel" file.

2- Kerneltype: An integer number that describes the type of kernel to

be used. For available kernel types see the "Implemented Kernels"

section below. For additional technical details see reference [1].

3- Asymptote: A real number that rescales the bond energy to the

correct dissociation energy. Due to the kernels implementiation, the

asympotic energy needs to go to zero.

!--------------------------------Description-------------------------------!

EXTBOND is invoked by the XTBD command. At first the module reads the

parameters for the new bond and the atoms involved. The new bond

definition will be considered only for the present run of CHARMM, no

modifications will be applied to the PSF file.

No modifications are needed in the parameter files.

No compatibility issues with other modules in CHARMM are registered.

!-----------------------------Parameter file-----------------------------!

The bond parameters can be given both: internally in the input file or

externally.

The definition of the bond in the external file is presented here.

The first line is an integer number that defines the number of bonds

present in the external file. The second and third lines define the

bond type and atoms involved with its parameters respectively. In the

next lines a dummy example can be found.

N ! number of bonds defined in the file

TYPE ! typology of bond

ATOM1 ATOM2 parameters ! atoms involved in the new bond and bond parameters.

repeat the second and third line N-1 times.

Example::

!--- CHARMM input file

... parameters defintions....

open unit 40 card name yourdatafile

XTBD read unit 40

... the rest of the input

HARM

1 2 600.00 1.23

AMOE

3 4 600.00 1.23

MORS

5 6 120.0 1.21 2.7

QUAR

7 8 110.0 1.2 50. 20.0

RKHS

9 10 pes 0 K1D -121.9746

!-------------------------Implemented Kernels-------------------------!

For more details see reference [1].

0 -> Reciprocal Power N2 M6 Kernel

1 -> Reciprocal Power N3 M6 Kernel

2 -> Reciprocal Power N2 M5 Kernel

3 -> Reciprocal Power N3 M5 Kernel

4 -> Reciprocal Power N2 M4 Kernel

5 -> Reciprocal Power N3 M4 Kernel

6 -> Reciprocal Power N2 M3 Kernel

7 -> Reciprocal Power N3 M3 Kernel

8 -> Reciprocal Power N2 M2 Kernel

9 -> Reciprocal Power N3 M2 Kernel

10 -> Reciprocal Power N2 M1 Kernel

11 -> Reciprocal Power N3 M1 Kernel

12 -> Reciprocal Power N2 M0 Kernel

13 -> Reciprocal Power N3 M0 Kernel

14 -> Exponetial Decay N2 kernel

15 -> Exponetial Decay N2 kernel

N describes the number of terms used in the Kernels, M describes the

degree of the polynomial expansion.

Reciprocal Power Decay:: Those kernels describe a decay of the form of

1/r^(m+1) decay for values larger than the greatest point in the

grid. The kernel is defined for values on the interval [0,infinity).

Laplacian:: Necessary to evaluate the Laplacian kernel given by

exp(||x-x'||/sigma). Note that sigma can be set to any positive

value, but is initialized automatically with the value 1. It is not

recommended for interpolating potential energy surfaces. The kernel is

only defined on the interval [0,infinity).

Exponential Decay:: For values larger than the greatest point in the

grid, the kernel decays exponentially with exp(-beta*x). Note that

beta can be set to any positive value, but is initialized

automatically with the value 1. This type of kernel is recommended

for short-range intermolecular interactions, which often decay

exponentially. The kernel is only defined for values in the interval

[0,infinity).

For most applications a chemical bond can be described by a Reciprocal

Power N2 M6 Kernel (option "0").

!------------------------- How to build a grid-------------------------!

1) For each bond that should be reproduced by a kernel, perform an Ab

Initio calculation along a scan of the bond.

2) Save the bond length and the energies (in AKMA units), in

increasing order of r in a csv file.

r1 , E1

r2 , E2

....

rN , EN

3) Reference the energies to the asymptote E - E_asympt, such that

E(r_asympt)=0.

!-----------------------------------Example-----------------------------------!

The xtbd_nma.inp test case with the parameter xtbd_nma.para parameter

file and the xtbd_pes.csv, that contains the kernel, are distributed

with the package. This example describes the vibrational analysis and

free dynamics of the NMA molecule with the EXTBOND module invoked for

the C=O bond.