# crystl (c47b2)

Calculations on Crystals using CHARMM

The crystal section within CHARMM allows calculations on

crystals to be performed. It is possible to build a crystal with any

space group symmetry, to optimise its lattice parameters and molecular

coordinates and to carry out a vibrational analysis using the options.

* Syntax | Syntax of the CRYSTAL command

* Function | A brief description of each command

* Examples | Sample testcases

* Implementation | Background and implementation

The crystal section within CHARMM allows calculations on

crystals to be performed. It is possible to build a crystal with any

space group symmetry, to optimise its lattice parameters and molecular

coordinates and to carry out a vibrational analysis using the options.

* Syntax | Syntax of the CRYSTAL command

* Function | A brief description of each command

* Examples | Sample testcases

* Implementation | Background and implementation

Top

[Syntax CRYStal command]

CRYStal [BUILd_crystal] [CUTOff real] [NOPErations int]

[DEFIne xtltyp a b c alpha beta gamma]

[FREE]

[PHONon] [NKPOints int]

[KVECtor real real real TO real real real]

[VIBRation]

[READ] [CARD UNIT int]

[PHONons UNIT int]

[PRINt]

[PRINt] [PHONons] [FACT real] [MODE int THRU int]

[KPTS int TO int]

[WRITe] [CARD UNIT int]

[PHONons UNIT int]

[VIBRations] [MODE int THRU int] [UNIT int]

xtltyp ::= { CUBIc }

{ TETRagonal }

{ ORTHorhombic }

{ MONOclinic }

{ TRIClinic }

{ HEXAgonal }

{ RHOMohedral }

{ OCTAhedral/trnc}

{ RHDO }

a b c alpha beta gamma ::= (six real numbers)

The crystal module is an extension of the image facility

within the CHARMM program. All crystal commands are invoked by the

keyword CRYStal. The next word on the command line can be one of the

following :

Build - builds a crystal.

Define - defines the lattice type and constants of the crystal to be

studied.

Free - clear the crystal and image facility.

Phonon - calculates the crystal frequencies for a single value or a

range of values of the wave vector, KVEC.

Print - prints various crystal information.

Read - reads the crystal image file.

Vibration - calculates the harmonic crystal frequencies when the wave

vector is the zero vector.

Write - writes out to file various crystal information.

[Syntax CRYStal command]

CRYStal [BUILd_crystal] [CUTOff real] [NOPErations int]

[DEFIne xtltyp a b c alpha beta gamma]

[FREE]

[PHONon] [NKPOints int]

[KVECtor real real real TO real real real]

[VIBRation]

[READ] [CARD UNIT int]

[PHONons UNIT int]

[PRINt]

[PRINt] [PHONons] [FACT real] [MODE int THRU int]

[KPTS int TO int]

[WRITe] [CARD UNIT int]

[PHONons UNIT int]

[VIBRations] [MODE int THRU int] [UNIT int]

xtltyp ::= { CUBIc }

{ TETRagonal }

{ ORTHorhombic }

{ MONOclinic }

{ TRIClinic }

{ HEXAgonal }

{ RHOMohedral }

{ OCTAhedral/trnc}

{ RHDO }

a b c alpha beta gamma ::= (six real numbers)

The crystal module is an extension of the image facility

within the CHARMM program. All crystal commands are invoked by the

keyword CRYStal. The next word on the command line can be one of the

following :

Build - builds a crystal.

Define - defines the lattice type and constants of the crystal to be

studied.

Free - clear the crystal and image facility.

Phonon - calculates the crystal frequencies for a single value or a

range of values of the wave vector, KVEC.

Print - prints various crystal information.

Read - reads the crystal image file.

Vibration - calculates the harmonic crystal frequencies when the wave

vector is the zero vector.

Write - writes out to file various crystal information.

Top

A brief description of each command follows.

1. Crystal Build.

A crystal of any desired symmetry can be constructed by repeatedly

applying a small number of transformations to an asymmetric collection of

atoms (called here the primary atoms). The transformations include the

primitive lattice translations A, B and C which are common to all crystals

and a set of additional transformations, {T}, which determines the space

group symmetry.

The Build command will generate, given {T}, a data structure of all

those transformations which produce images lying within a user-specified

cutoff distance of the primary atoms. The data structure can then be used

by CHARMM to represent the complete crystal of the system in subsequent

calculations. The symmetry operations, {T}, are read from the lines

following the Crystal Build command.

The syntax of the commmand is :

Crystal Build Cutoff <real> Noperations <int>

... <int> lines defining the symmmetry operations.

The Cutoff parameter is used to determine the images which are included

in the transformation list. All those images which are within the cutoff

distance are included in the list. Note: The distance test is done based on

the atoms that are currently present and their symmetric representation.

To generate a crystal file from a box with a single atom at the center,

the cutoff value will nee to be larger than the box dimensions. If the

box is filled with water and only nearest neighbor cells are desired,

then the cutoff distance should be comparable to the CUTIM value

(see

(see

number of transformations included in the lists as they are allocated

dynamically, but having too many will slow the image update step.

The crystal symmetry operations are input in standard crystallographic

notation. The identity is assumed to be present so that (X,Y,Z) need not

be specified (in fact, it is an error to do so). For example, a P1

crystal is defined by the identity operation and so the input would be

Crystal Build .... Noper 0

whilst a P21 crystal would need the following input lines :

Crystal Build .... Noper 1

(-X,Y+1/2,-Z)

A P212121 crystal is specified by Noper 3

(X+1/2,-Y+1/2,-Z)

(-X,Y+1/2,-Z+1/2)

(-X+1/2,-Y,Z+1/2)

It should be noted that in those cases where the atoms in the

asymmetric unit have internal symmetry or in which a molecule is sited

upon a symmetry point within the unit cell not all symmetry

transformations for the crystal need to be input. Some will be

redundant. It is up to the user to check for these cases and modify

the input accordingly.

2. Crystal Define.

The define command defines the crystal-type on which calculations

are to be performed. It is usually the first crystal command that is

specified in any job using the crystal facility. It has the format :

Define lattice-type a b c alpha beta gamma

The input lattice parameters are checked against the lattice-type to

ensure that they are compatible. Nine lattice types are permitted. They

are listed below along with any restrictions on the lattice parameters :

CUBIc - a = b = c and alpha = beta = gamma = 90.0 degrees.

(example: 50.0 50.0 50.0 90.0 90.0 90.0 )

(volume = a**3)

(degrees of freedom = 1)

TETRagonal - a = b and alpha = beta = gamma = 90.0 degrees.

(example: 50.0 50.0 40.0 90.0 90.0 90.0 )

(volume = c*a**2)

(degrees of freedom = 2)

ORTHorhombic - alpha = beta = gamma = 90.0 degrees.

(example: 50.0 40.0 30.0 90.0 90.0 90.0 )

(volume = c*b*a)

(degrees of freedom = 3)

MONOclinic - alpha = gamma = 90.0 degrees.

(example: 50.0 40.0 30.0 90.0 70.0 90.0 )

(volume = c*b*a*sin(beta) )

(degrees of freedom = 4)

TRIClinic - no restrictions on a, b, c, alpha, beta or gamma.

(example: 50.0 40.0 30.0 60.0 70.0 80.0 )

(volume = c*b*a*sqrt(1.0 - cos(alpha)**2 - cos(beta)**2 -

cos(gamma)**2 + 2.0*cos(alpha)*cos(beta)*cos(gamma)) )

(degrees of freedom = 6)

HEXAgonal - a = b, alpha = beta = 90.0 degrees and gamma = 120.0

(example: 40.0 40.0 120.0 90.0 90.0 120.0 )

(volume = sqrt(0.75)*c*a**2 )

(degrees of freedom = 2)

RHOMbohedral - a = b = c ; alpha=beta=gamma<120 (trigonal)

(example: 40.0 40.0 40.0 67.0 67.0 67.0 )

(volume = a**3*(1.0-cos(alpha))*sqrt(1.0+2.0*cos(alpha)) )

(degrees of freedom = 2)

OCTAhedral - a = b = c, alpha = beta = gamma = 109.4712206344907

(a.k.a truncated octahedron)

(example: 40.0 40.0 40.0 109.471220634 109.471220634 109.471220634 )

(volume = 4*sqrt(3))/9 * a**3 )

(truncated cube length = a * sqrt(4/3) )

(degrees of freedom = 1)

RHDO (Rhombic Dodecahedron)

- a = b = c, alpha = gamma = 60.0 and beta = 90.0

(example: 40.0 40.0 40.0 60.0 90.0 60.0 )

(volume = sqrt(0.5) * a**3 )

(truncated cube length = a * sqrt(2) )

(degrees of freedom = 1)

It is up to the user to ensure that the lattice parameters have the

desired values for the system at all times. The values are stored

by the program but, at present, the only way to transmit this information

between jobs is with binary coordinate, trajectory, or restart files.

For example, if the lattice parameters have been changed during a

lattice optimization then the new parameters, which are printed out at

the end of the minimization, must be input at the beginning of

the next CHARMM run, or transferred using the FILE option on coordinate

writing and reading. Lattice parameters are stored in binary coordinate,

dynamic trajectory, and restart files only.

3. Crystal Phonon.

Phonon calculates the dispersion curves for a crystal. Any value

of the wavevector can be used (although, in practice, each component

of KVEC is normally limited to the range -0.5 to +0.5). The dynamical

matrix and normal mode eigenvectors determined in the phonon

calculation are complex although the eigenvalues remain real.

The syntax for the command is :

Crystal Phonon Nkpoints <i> Kvector <f> <f> <f> To <f> <f> <f>

Nkpoints tells the program the number of points at which the derivative

matrices must be built and diagonalised whilst the Kvector ... To ...

clause determines the values of KVEC for each calculation. Thus,

Kvector 0.0 0.0 0.0 To 0.5 0.5 0.5 Nkpoints 3

would solve for the crystal frequencies at the points, KVEC=(0.0,0.0,0.0),

(0.25,0.25,0.25) and (0.5,0.5,0.5). If it is desirable, point calculations

can be carried out by omitting the To statement and putting Nkpoints 1.

For single calculations at KVEC=(0.0,0.0,0.0) the Crystal Vibration command

is faster.

The eigenvalues and eigenvectors at each value of the wave vector

from the phonon calculation are saved and they can be written out to a

file using the Crystal Write Phonon command. No analysis facilities

exist within CHARMM for the phonon data structure as the eigenvectors

are complex.

It is to be noted that phonon and vibration calculations can only

be performed on crystals of P1 symmetry. No information about the

symmetry operations is used when generating the dynamical matrix.

4. Crystal Print.

Two options exist with the Print command. If no keyword is given

then the crystal image file is printed out.

The Crystal Print Phonon command performs a similar function to the

Print Normal_Modes command in the vibrational analysis facility. Selected

frequencies and eigenvectors for a range of values of the wave vector can

be printed out. The syntax is :

Crystal Print Phonon Kpoints <i> To <i> Modes <i> Thru <i> Factor <f>

The Kpoints .. To .. clause determines the wave-vectors at which the

modes are to be printed, the Modes .. Thru .. gives the range of the

eigenvectors and the Factor command gives the scale factor to multiply

each normal mode by.

5. Crystal Read.

The Crystal Read command reads in a crystal image file. The file

has the same output as produced by the Crystal Print or Crystal Write

commands. The command is useful if a crystal image file was produced

using the Crystal Build command and saved using the Crystal Write

command in a previous job and it is desired to reuse the same

transformation file for analysis or comparison purposes. The command

can also be used to read in limited sets of transformations if

specific crystal interactions need to be investigated. The

transformation file is formatted so the Card keyword needs to be

specified and the unit number must be given after the Unit keyword.

6. Crystal Vibration.

For a free molecule with N atoms the dynamical equations have 3N-6

non-zero eigenvalues. This is no longer so for a crystal. If a crystal

is made up of L unit cells each containing Z molecules with N atoms,

the dynamical equations would have a dimension of 3NZL. However, using

the symmetry properties of the lattice it is possible to factor the

equations into L sets each with a dimension of 3NZ and each depending

upon a vector, KVEC, which labels the irreducible representation of the

translation group to which the set belongs. The force constant matrix

is complex. Its form may be found in the references given at the end of

the documentation.

Vibration solves the dynamical equations for the case where the wave-vector

is zero, i.e. when the equations are real. The procedure is invoked by the

Crystal Vibration command. The syntax is :

Crystal Vibration

7. Crystal Write.

There are three Crystal Write options. If no keyword is given the

crystal image file is written out, in card format, to the specified

unit. The CARD and UNIT keywords are required.

The Crystal Write Phonon command writes out the phonons from a

phonon calculation. All the eigenvalues and eigenvectors for all

values of the wavevector that are stored are written automatically.

The Crystal Write Vibration command writes out the eigenvalues and

eigenvectors from a vibration calculation. The modes to be written are

given by the Mode .. Thru .. clause.

All Write commands require that the Fortran stream number be given

after the Unit keyword and a CHARMM title may be specified on the

following lines.

The structure of the phonon and vibration files for a crystal may

be found by looking at the routines WRITDC and XFRQW2 respectively

in the file [.IMAGE]XTLFRQ.SRC. The vibration modes are written

in the same form as a for VIBRAN normal mode file and may be read

in using the appropriate VIBRAN commands. Unfortunately no analysis

facilities exist for complex eigenvectors within CHARMM and so users

will have to write their own if they want to perform phonon

calculations.

8. Crystal Minimization.

It is possible to perform a lattice minimization using the normal

have been introduced. If none of them is present then a coordinate

minimization is performed as usual. If LATTICE is specified then

the LATTice parameters and the atomic coordinates are minimized

together. If NOCOoordinates is given with the keyword LATTice then

only the lattice parameters are optimised. Specifying NOCOordinates

by itself is an error.

It should be noted that when the lattice is being optimised the

crystal symmetry is maintained. A cubic crystal will remain cubic, etc.

A brief description of each command follows.

1. Crystal Build.

A crystal of any desired symmetry can be constructed by repeatedly

applying a small number of transformations to an asymmetric collection of

atoms (called here the primary atoms). The transformations include the

primitive lattice translations A, B and C which are common to all crystals

and a set of additional transformations, {T}, which determines the space

group symmetry.

The Build command will generate, given {T}, a data structure of all

those transformations which produce images lying within a user-specified

cutoff distance of the primary atoms. The data structure can then be used

by CHARMM to represent the complete crystal of the system in subsequent

calculations. The symmetry operations, {T}, are read from the lines

following the Crystal Build command.

The syntax of the commmand is :

Crystal Build Cutoff <real> Noperations <int>

... <int> lines defining the symmmetry operations.

The Cutoff parameter is used to determine the images which are included

in the transformation list. All those images which are within the cutoff

distance are included in the list. Note: The distance test is done based on

the atoms that are currently present and their symmetric representation.

To generate a crystal file from a box with a single atom at the center,

the cutoff value will nee to be larger than the box dimensions. If the

box is filled with water and only nearest neighbor cells are desired,

then the cutoff distance should be comparable to the CUTIM value

(see

**»**images Update.) or the CUTNB value(see

**»**nbonds Syntax.). There is no limit to thenumber of transformations included in the lists as they are allocated

dynamically, but having too many will slow the image update step.

The crystal symmetry operations are input in standard crystallographic

notation. The identity is assumed to be present so that (X,Y,Z) need not

be specified (in fact, it is an error to do so). For example, a P1

crystal is defined by the identity operation and so the input would be

Crystal Build .... Noper 0

whilst a P21 crystal would need the following input lines :

Crystal Build .... Noper 1

(-X,Y+1/2,-Z)

A P212121 crystal is specified by Noper 3

(X+1/2,-Y+1/2,-Z)

(-X,Y+1/2,-Z+1/2)

(-X+1/2,-Y,Z+1/2)

It should be noted that in those cases where the atoms in the

asymmetric unit have internal symmetry or in which a molecule is sited

upon a symmetry point within the unit cell not all symmetry

transformations for the crystal need to be input. Some will be

redundant. It is up to the user to check for these cases and modify

the input accordingly.

2. Crystal Define.

The define command defines the crystal-type on which calculations

are to be performed. It is usually the first crystal command that is

specified in any job using the crystal facility. It has the format :

Define lattice-type a b c alpha beta gamma

The input lattice parameters are checked against the lattice-type to

ensure that they are compatible. Nine lattice types are permitted. They

are listed below along with any restrictions on the lattice parameters :

CUBIc - a = b = c and alpha = beta = gamma = 90.0 degrees.

(example: 50.0 50.0 50.0 90.0 90.0 90.0 )

(volume = a**3)

(degrees of freedom = 1)

TETRagonal - a = b and alpha = beta = gamma = 90.0 degrees.

(example: 50.0 50.0 40.0 90.0 90.0 90.0 )

(volume = c*a**2)

(degrees of freedom = 2)

ORTHorhombic - alpha = beta = gamma = 90.0 degrees.

(example: 50.0 40.0 30.0 90.0 90.0 90.0 )

(volume = c*b*a)

(degrees of freedom = 3)

MONOclinic - alpha = gamma = 90.0 degrees.

(example: 50.0 40.0 30.0 90.0 70.0 90.0 )

(volume = c*b*a*sin(beta) )

(degrees of freedom = 4)

TRIClinic - no restrictions on a, b, c, alpha, beta or gamma.

(example: 50.0 40.0 30.0 60.0 70.0 80.0 )

(volume = c*b*a*sqrt(1.0 - cos(alpha)**2 - cos(beta)**2 -

cos(gamma)**2 + 2.0*cos(alpha)*cos(beta)*cos(gamma)) )

(degrees of freedom = 6)

HEXAgonal - a = b, alpha = beta = 90.0 degrees and gamma = 120.0

(example: 40.0 40.0 120.0 90.0 90.0 120.0 )

(volume = sqrt(0.75)*c*a**2 )

(degrees of freedom = 2)

RHOMbohedral - a = b = c ; alpha=beta=gamma<120 (trigonal)

(example: 40.0 40.0 40.0 67.0 67.0 67.0 )

(volume = a**3*(1.0-cos(alpha))*sqrt(1.0+2.0*cos(alpha)) )

(degrees of freedom = 2)

OCTAhedral - a = b = c, alpha = beta = gamma = 109.4712206344907

(a.k.a truncated octahedron)

(example: 40.0 40.0 40.0 109.471220634 109.471220634 109.471220634 )

(volume = 4*sqrt(3))/9 * a**3 )

(truncated cube length = a * sqrt(4/3) )

(degrees of freedom = 1)

RHDO (Rhombic Dodecahedron)

- a = b = c, alpha = gamma = 60.0 and beta = 90.0

(example: 40.0 40.0 40.0 60.0 90.0 60.0 )

(volume = sqrt(0.5) * a**3 )

(truncated cube length = a * sqrt(2) )

(degrees of freedom = 1)

It is up to the user to ensure that the lattice parameters have the

desired values for the system at all times. The values are stored

by the program but, at present, the only way to transmit this information

between jobs is with binary coordinate, trajectory, or restart files.

For example, if the lattice parameters have been changed during a

lattice optimization then the new parameters, which are printed out at

the end of the minimization, must be input at the beginning of

the next CHARMM run, or transferred using the FILE option on coordinate

writing and reading. Lattice parameters are stored in binary coordinate,

dynamic trajectory, and restart files only.

3. Crystal Phonon.

Phonon calculates the dispersion curves for a crystal. Any value

of the wavevector can be used (although, in practice, each component

of KVEC is normally limited to the range -0.5 to +0.5). The dynamical

matrix and normal mode eigenvectors determined in the phonon

calculation are complex although the eigenvalues remain real.

The syntax for the command is :

Crystal Phonon Nkpoints <i> Kvector <f> <f> <f> To <f> <f> <f>

Nkpoints tells the program the number of points at which the derivative

matrices must be built and diagonalised whilst the Kvector ... To ...

clause determines the values of KVEC for each calculation. Thus,

Kvector 0.0 0.0 0.0 To 0.5 0.5 0.5 Nkpoints 3

would solve for the crystal frequencies at the points, KVEC=(0.0,0.0,0.0),

(0.25,0.25,0.25) and (0.5,0.5,0.5). If it is desirable, point calculations

can be carried out by omitting the To statement and putting Nkpoints 1.

For single calculations at KVEC=(0.0,0.0,0.0) the Crystal Vibration command

is faster.

The eigenvalues and eigenvectors at each value of the wave vector

from the phonon calculation are saved and they can be written out to a

file using the Crystal Write Phonon command. No analysis facilities

exist within CHARMM for the phonon data structure as the eigenvectors

are complex.

It is to be noted that phonon and vibration calculations can only

be performed on crystals of P1 symmetry. No information about the

symmetry operations is used when generating the dynamical matrix.

4. Crystal Print.

Two options exist with the Print command. If no keyword is given

then the crystal image file is printed out.

The Crystal Print Phonon command performs a similar function to the

Print Normal_Modes command in the vibrational analysis facility. Selected

frequencies and eigenvectors for a range of values of the wave vector can

be printed out. The syntax is :

Crystal Print Phonon Kpoints <i> To <i> Modes <i> Thru <i> Factor <f>

The Kpoints .. To .. clause determines the wave-vectors at which the

modes are to be printed, the Modes .. Thru .. gives the range of the

eigenvectors and the Factor command gives the scale factor to multiply

each normal mode by.

5. Crystal Read.

The Crystal Read command reads in a crystal image file. The file

has the same output as produced by the Crystal Print or Crystal Write

commands. The command is useful if a crystal image file was produced

using the Crystal Build command and saved using the Crystal Write

command in a previous job and it is desired to reuse the same

transformation file for analysis or comparison purposes. The command

can also be used to read in limited sets of transformations if

specific crystal interactions need to be investigated. The

transformation file is formatted so the Card keyword needs to be

specified and the unit number must be given after the Unit keyword.

6. Crystal Vibration.

For a free molecule with N atoms the dynamical equations have 3N-6

non-zero eigenvalues. This is no longer so for a crystal. If a crystal

is made up of L unit cells each containing Z molecules with N atoms,

the dynamical equations would have a dimension of 3NZL. However, using

the symmetry properties of the lattice it is possible to factor the

equations into L sets each with a dimension of 3NZ and each depending

upon a vector, KVEC, which labels the irreducible representation of the

translation group to which the set belongs. The force constant matrix

is complex. Its form may be found in the references given at the end of

the documentation.

Vibration solves the dynamical equations for the case where the wave-vector

is zero, i.e. when the equations are real. The procedure is invoked by the

Crystal Vibration command. The syntax is :

Crystal Vibration

7. Crystal Write.

There are three Crystal Write options. If no keyword is given the

crystal image file is written out, in card format, to the specified

unit. The CARD and UNIT keywords are required.

The Crystal Write Phonon command writes out the phonons from a

phonon calculation. All the eigenvalues and eigenvectors for all

values of the wavevector that are stored are written automatically.

The Crystal Write Vibration command writes out the eigenvalues and

eigenvectors from a vibration calculation. The modes to be written are

given by the Mode .. Thru .. clause.

All Write commands require that the Fortran stream number be given

after the Unit keyword and a CHARMM title may be specified on the

following lines.

The structure of the phonon and vibration files for a crystal may

be found by looking at the routines WRITDC and XFRQW2 respectively

in the file [.IMAGE]XTLFRQ.SRC. The vibration modes are written

in the same form as a for VIBRAN normal mode file and may be read

in using the appropriate VIBRAN commands. Unfortunately no analysis

facilities exist for complex eigenvectors within CHARMM and so users

will have to write their own if they want to perform phonon

calculations.

8. Crystal Minimization.

It is possible to perform a lattice minimization using the normal

have been introduced. If none of them is present then a coordinate

minimization is performed as usual. If LATTICE is specified then

the LATTice parameters and the atomic coordinates are minimized

together. If NOCOoordinates is given with the keyword LATTice then

only the lattice parameters are optimised. Specifying NOCOordinates

by itself is an error.

It should be noted that when the lattice is being optimised the

crystal symmetry is maintained. A cubic crystal will remain cubic, etc.

Top

Examples of input may be found in the test directory. All crystal

files are prefixed by the string "xtl_". All the jobs involve

L-Alanine. Briefly the jobs are :

1. XTL_ALA1.INP. The crystallographic fractional coordinates are

read in and converted to real space coordinates

using the CHARMM COORdinate CONVert command and

the experimental values for the lattice parameters.

2. XTL_ALA2.INP. A crystal image file is generated for the crystal

using a value of 10.0 Angstroms for the crystal

cutoff.

3. XTL_ALA3.INP. A coordinate and lattice minimization are performed

for the crystal. The crystal image file from the

previous job is used and the optimised coordinates

are saved. The main point to note is that before

using the crystal package for energy calculations

and other manipulations that involve the image

non-bond lists an image update must be performed.

For safety always do an update after building or

reading in the crystal. Note too that the new,

optimised lattice parameters are used in the all

the subsequent input files.

4. XTL_ALA4.INP. For subsequent calculations a coordinate file that

contains the coordinates of all atoms (four

molecules of L-alanine) is generated. A crystal

image file suitable to do this is read in directly

from the input stream. It contains 6 transformations

(not 3 as might be expected) because the CHARMM

image facility requires that the inverses of all

transformations be present. The first three are the

ones needed and the last three are their inverses.

An update is needed after reading the file to make

known to the program the coordinates of the atoms

in the first transformation of all the inverse pairs

in the image list. The Print Coor Image file will

then print out the coordinates of the atoms in the

original asymmetric unit and the first three of the

images. If the coordinates of the atoms in all the

images are required then the keyword NOINV in the

UPDATE command must be used (check IMAGE.DOC).

5. XTL_ALA5.INP. The same job as the second except that the crystal

is generated for a whole unit cell (i.e. the system

generated in the fourth job). The same value of the

crystal cutoff is used. An energy is calculated too.

The energy and its RMS coordinate derivative should

be exactly four times (apart from a small round-off

error) the value obtained for an energy calculation

on a single asymmetric unit with the same lattice

parameters and crystal cutoff (see job 3).

6. XTL_ALA6.INP. Peform a crystal vibration and phonon calculation

for the optimised structure of the L-alanine

crystal. The vibrational and phonon modes are

written out to files and components of the first 24

phonon normal modes for the three values of the

wavevector that were calculated are printed. To

do the same for the vibrations it would be necessary

to use the appropriate VIBRAN commands in another

job.

Advanced example: Applying P21 Symmetry to Interfacial Systems

A slightly more novel application of crystal symmetry is the use of

P21 symmetry for systems with planar interfaces, notably lipid bilayers

and related multiphase systems. The general idea is that the simulation

cell is an asymmetric unit, replicated through rotational symmetry such

that the interface becomes one continuous surface. A tetragonal unit

cell is required, and the interfaces must be in the XY plane and

symmetric wrt. the X=0,Y=0 plane.

The initial coordinate transform needed is straighforward, but the result

must be carefully minimized before use; the molecules in contact at the

AC and BC faces of the prism are completely changed by the rotational

symmetry. Assuming that a standard tetragonal prism has been set up,

the interconversion P1 ==> P21 can be accomplished via:

! COMPUTE NEW SIZE

calc a = sqrt(2) * ?XTLA

calc a4 = 0.25 * @A

set c = ?XTLC

! CHANGE BOX ORIENTATION, PLACEMENT

coor rotat zdir 1.0 phi 45.0

coor trans xdir @A4

! ESTABLISH NEW P21 SYMMETRY, AND APPLY IMAGE UPDATE

crystal free

crystal define tetra @A @A @C 90. 90. 90.

crystal build noper 1 cutoff 30.

(-X,Y+1/2,-Z)

image byres sele .not. segid a .or. segid b end xcen @A4 ! EXCLUDE PROTEIN

update cutim 15.

and the reverse transformation P21 ==> P1 can be done by:

! SETUP FOR SYMMETRY CHANGE; REPOSITION COORDS

calc a ?XTLA / sqrt(2.)

set c ?XTLC

calc a4 0.25 * ?XTLA

coor tran xdir -@A4

coor rota zdir 1. phi -45.

! ESTABLISH NEW P1 SYMMETRY, AND APPLY IMAGE UPDATE

crystal free

crystal define tetra @A @A @C 90. 90. 90.

crystal build noper 0 cutoff 30.

image byres sele .not. segid a .or. segid b end ! EXCLUDE PROTEIN

update cutim 15.

One approach to dealing with the changed molecular interactions for the AC

and BC faces is a staged reduction of the A and B edge lengths (where A=B

for the tetragonal prism). For lipid bilayer systems, it can also be

prudent to restrain the headgroup conformations during the minimization.

The following illustrates the use of CONS IC DIHE during a staged

reduction of the box size:

! QUICK IC TABLE FOR GLYCEROL BASED TORSIONS

ic generate sele segid LPD end

ic keep sele atom LPD * C+ end ! LIPID C1, C2, C3

ic delete sele type hydrogen end

cons ic dihe 1000.

! P1 MINIMIZATION LOOP; INCREDIBLE SHRINKING BOX

calc mxa @A + 4. + 2. + 1. + 0.5

set m 8

label minloop

! NEW SYMMETRY WITH AVG CELL CONSTANTS, UPDATE APPLIED

crystal free

crystal define tetragonal @MXA @MXA @C 90. 90. 90.

crystal build noper 0 cutoff 30.

calc A4 0.25 * @MXA

image byres sele .not. segid a .or. segid b end xcen @A4 ! EXCLUDE PROTEIN

! MINIMIZE; SHORT SD, THEN ABNR

mini sd nstep 50 nprint 5 -

inbfrq 10 atom vatom cutnb 14.0 ctofnb 12. cdie eps 1. -

ctonnb 8. vswitch cutim 14.0 imgfrq 10 wmin 0.5 -

ewald pmew fftx 80 ffty 80 fftz 80 kappa .34 spline order 6

mini abnr nstep 200 nprint 10

! SIZE REDUCTION AND LOOP TEST

calc mxa = @MXA - ( @M * 0.5 )

calc m = @M / 2

if m .ge. 1 goto minloop

Finally, for use with NPT simulations where the A=B edges can change,

the P21XCEN keyword » pressure keyword enables automatic

adjustment of the image centering XCEN value to be 0.25*A as the edge

values change during the course of dynamics.

Simulations of Membranes and Other Interfacial Systems Using P21

and Pc Periodic Boundary Conditions

EA Dolan, RM Venable, RW Pastor, and BR Brooks

Biophys. J. 82:2317-2325 (2002)

Examples of input may be found in the test directory. All crystal

files are prefixed by the string "xtl_". All the jobs involve

L-Alanine. Briefly the jobs are :

1. XTL_ALA1.INP. The crystallographic fractional coordinates are

read in and converted to real space coordinates

using the CHARMM COORdinate CONVert command and

the experimental values for the lattice parameters.

2. XTL_ALA2.INP. A crystal image file is generated for the crystal

using a value of 10.0 Angstroms for the crystal

cutoff.

3. XTL_ALA3.INP. A coordinate and lattice minimization are performed

for the crystal. The crystal image file from the

previous job is used and the optimised coordinates

are saved. The main point to note is that before

using the crystal package for energy calculations

and other manipulations that involve the image

non-bond lists an image update must be performed.

For safety always do an update after building or

reading in the crystal. Note too that the new,

optimised lattice parameters are used in the all

the subsequent input files.

4. XTL_ALA4.INP. For subsequent calculations a coordinate file that

contains the coordinates of all atoms (four

molecules of L-alanine) is generated. A crystal

image file suitable to do this is read in directly

from the input stream. It contains 6 transformations

(not 3 as might be expected) because the CHARMM

image facility requires that the inverses of all

transformations be present. The first three are the

ones needed and the last three are their inverses.

An update is needed after reading the file to make

known to the program the coordinates of the atoms

in the first transformation of all the inverse pairs

in the image list. The Print Coor Image file will

then print out the coordinates of the atoms in the

original asymmetric unit and the first three of the

images. If the coordinates of the atoms in all the

images are required then the keyword NOINV in the

UPDATE command must be used (check IMAGE.DOC).

5. XTL_ALA5.INP. The same job as the second except that the crystal

is generated for a whole unit cell (i.e. the system

generated in the fourth job). The same value of the

crystal cutoff is used. An energy is calculated too.

The energy and its RMS coordinate derivative should

be exactly four times (apart from a small round-off

error) the value obtained for an energy calculation

on a single asymmetric unit with the same lattice

parameters and crystal cutoff (see job 3).

6. XTL_ALA6.INP. Peform a crystal vibration and phonon calculation

for the optimised structure of the L-alanine

crystal. The vibrational and phonon modes are

written out to files and components of the first 24

phonon normal modes for the three values of the

wavevector that were calculated are printed. To

do the same for the vibrations it would be necessary

to use the appropriate VIBRAN commands in another

job.

Advanced example: Applying P21 Symmetry to Interfacial Systems

A slightly more novel application of crystal symmetry is the use of

P21 symmetry for systems with planar interfaces, notably lipid bilayers

and related multiphase systems. The general idea is that the simulation

cell is an asymmetric unit, replicated through rotational symmetry such

that the interface becomes one continuous surface. A tetragonal unit

cell is required, and the interfaces must be in the XY plane and

symmetric wrt. the X=0,Y=0 plane.

The initial coordinate transform needed is straighforward, but the result

must be carefully minimized before use; the molecules in contact at the

AC and BC faces of the prism are completely changed by the rotational

symmetry. Assuming that a standard tetragonal prism has been set up,

the interconversion P1 ==> P21 can be accomplished via:

! COMPUTE NEW SIZE

calc a = sqrt(2) * ?XTLA

calc a4 = 0.25 * @A

set c = ?XTLC

! CHANGE BOX ORIENTATION, PLACEMENT

coor rotat zdir 1.0 phi 45.0

coor trans xdir @A4

! ESTABLISH NEW P21 SYMMETRY, AND APPLY IMAGE UPDATE

crystal free

crystal define tetra @A @A @C 90. 90. 90.

crystal build noper 1 cutoff 30.

(-X,Y+1/2,-Z)

image byres sele .not. segid a .or. segid b end xcen @A4 ! EXCLUDE PROTEIN

update cutim 15.

and the reverse transformation P21 ==> P1 can be done by:

! SETUP FOR SYMMETRY CHANGE; REPOSITION COORDS

calc a ?XTLA / sqrt(2.)

set c ?XTLC

calc a4 0.25 * ?XTLA

coor tran xdir -@A4

coor rota zdir 1. phi -45.

! ESTABLISH NEW P1 SYMMETRY, AND APPLY IMAGE UPDATE

crystal free

crystal define tetra @A @A @C 90. 90. 90.

crystal build noper 0 cutoff 30.

image byres sele .not. segid a .or. segid b end ! EXCLUDE PROTEIN

update cutim 15.

One approach to dealing with the changed molecular interactions for the AC

and BC faces is a staged reduction of the A and B edge lengths (where A=B

for the tetragonal prism). For lipid bilayer systems, it can also be

prudent to restrain the headgroup conformations during the minimization.

The following illustrates the use of CONS IC DIHE during a staged

reduction of the box size:

! QUICK IC TABLE FOR GLYCEROL BASED TORSIONS

ic generate sele segid LPD end

ic keep sele atom LPD * C+ end ! LIPID C1, C2, C3

ic delete sele type hydrogen end

cons ic dihe 1000.

! P1 MINIMIZATION LOOP; INCREDIBLE SHRINKING BOX

calc mxa @A + 4. + 2. + 1. + 0.5

set m 8

label minloop

! NEW SYMMETRY WITH AVG CELL CONSTANTS, UPDATE APPLIED

crystal free

crystal define tetragonal @MXA @MXA @C 90. 90. 90.

crystal build noper 0 cutoff 30.

calc A4 0.25 * @MXA

image byres sele .not. segid a .or. segid b end xcen @A4 ! EXCLUDE PROTEIN

! MINIMIZE; SHORT SD, THEN ABNR

mini sd nstep 50 nprint 5 -

inbfrq 10 atom vatom cutnb 14.0 ctofnb 12. cdie eps 1. -

ctonnb 8. vswitch cutim 14.0 imgfrq 10 wmin 0.5 -

ewald pmew fftx 80 ffty 80 fftz 80 kappa .34 spline order 6

mini abnr nstep 200 nprint 10

! SIZE REDUCTION AND LOOP TEST

calc mxa = @MXA - ( @M * 0.5 )

calc m = @M / 2

if m .ge. 1 goto minloop

Finally, for use with NPT simulations where the A=B edges can change,

the P21XCEN keyword » pressure keyword enables automatic

adjustment of the image centering XCEN value to be 0.25*A as the edge

values change during the course of dynamics.

Simulations of Membranes and Other Interfacial Systems Using P21

and Pc Periodic Boundary Conditions

EA Dolan, RM Venable, RW Pastor, and BR Brooks

Biophys. J. 82:2317-2325 (2002)

Top

Background and Implementation.

The Crystal options and their commands were described above. The present

section discusses relevant background material and briefly reviews the

methods used in the implementation. Some technical points are also made.

The crystal option is an extension to the CHARMM program. The source

code is in the directory [.IMAGE] whilst the crystal data structure is in

the file IMAGE.FCM. Two additional source code files have been added -

CRYSTL.SRC and XTLFRQ.SRC. Small modifications have been made to the

files ENERGY.SRC and EIMAGE.SRC.

CHARMM Images and the Crystal Image Data Structure.

As outlined above a crystal structure can be specified entirely

by the action of the primitive translations A, B and C, and a small set of

transformations, {T} (which themselves are functions of A, B and C), on an

asymmetric group of atoms. In CHARMM the calculation of the energy assumes

that there exists a cutoff distance beyond which all interactions between

particles are neglected so that when performing calculations on

supposedly infinite crystals only a limited portion of that crystal, i.e.

that portion containing those atoms within the cutoff distance of the

primary atoms, need be considered.

The CHARMM image option, of course, already enables the energies of

crystals to be calculated but the input required to use it to do so is

cumbersome and time consuming. It is a great simplification to include an

extra data structure that defines the crystal in terms of A, B and C and

{T}.

There are a number of advantages:

1. A crystal is regular so that its generation can be automated. All that

needs to be done is to systematically transform the primary atoms by

one of the set {T} and a linear combination of A, B and C.

The result is obviously best stored in terms of A, B, and C

rather than as absolute numerical values of the transformations.

2. It is essential to define a CHARMM crystal by A, B and C and {T} if the

lattice parameters a, b, c, alpha, beta and gamma are to be varied

because the coordinates of all the image atoms within the crystal will

change during successive cycles of the optimisation as a, b, c, alpha,

beta and gamma themselves change.

3. When constructing the dynamical matrix for a non-zero wave-vector it is

necessary to know the unit cell to which a particular atom belongs in

order to evaluate the exponential factor in the expression.

Although the crystal data structure and the values of the lattice

parameters define the crystal the individual transformations have to be

worked out explicitly in order to determine energies, harmonic frequencies

and so on. In the present version of the program the IMAGE facility is

used, so that a new set of IMAGE transformations are calculated from the

crystal data structure as soon as a crystal is built or every time the

lattice parameters are changed. The use of the IMAGE facility means that

the number of transformations that can be used is determined by the

dimension of the IMAGE arrays (MAXTRN in DIMENS.FCM).

Crystal and Image Patching, Image H-bonds

Crystal image patching is available in the present version of the

program, so that bonds between images are permitted, but with some

restrictions. The IMPAtch command requires the name of the image

transformation, so one *must* use CRYSTAL READ instead of CRYSTAL

BUILD, in order to preserve the names of the image transformations.

Hydrogen-bond interactions described by an explicit hydrogen-bond function

between primary and image atoms are forbidden.

The Lattice Coordinate System.

WARNING: If your system is not properly rotated, there will usually be

bad contacts. If you have bad contacts, check the alignment.

The convention used by CHARMM for orientating the crystal in real space involves

the use of a symmetric transformation (h) matrix. For non-orthorhombic systems,

these coordinates are different (rotated) from the aligned conventioned used by

PDB and others. The conversion is performed by the COOR CONVert command,

see

The Structure of the Crystal File.

The crystal file is divided into three parts.

A standard CHARMM title.

A symmetry operation declaration section headed by the word Symmetry

and terminated by an End. The transformations are written in the same

way as for the Crystal Build command except that the identity

transformation has to be explicitly listed.

An image section headed by Images and terminated by an End. Here the

images are defined in terms of the symmetry transformations and the

lattice translations A, B and C. The comment line shows the column

labelling.

Sometimes it is useful to write one's own crystal files without recourse

to the Crystal Build option. In this case the symmetry and image blocks

can be put in any order (although only one of each is allowed) and there

is no restriction on the positioning of blank and comment lines.

Two examples of a crystal file are:

* Crystal file for a P1bar crystal.

Symmetry

(X,Y,Z)

(-X,-Y,-Z)

End

Images

! Operation a b c

1 0 0 -1

1 0 0 1

2 0 0 0

End

* Crystal file for a P212121 crystal.

Symmetry

(X,Y,Z)

(X+1/2,-Y+1/2,-Z)

(-X,Y+1/2,-Z+1/2)

(-X+1/2,-Y,Z+1/2)

End

Images

! Operation a b c

2 0 0 0

3 0 0 0

4 0 0 0

2 -1 0 0

3 0 -1 0

4 0 0 -1

End

Second Derivative Calculations and the Use of Symmetry.

Consider a crystal with a unit cell in which there is more than one

asymmetric unit (i.e. all space groups other than P1). The dynamical

matrix then takes a blocked form, with Z**2 blocks if Z is the number

of asymmetric units. Each block is of dimension 3N x 3N and contains

the sum over all unit cells of the second derivative interaction

elements between the Mth and Nth asymmetric units. It is possible to

calculate only the Z blocks (11), (12), ..., (1M), ..., (1Z) and then

transform them to produce the full matrix. In the present program,

however, it is necessary to perform vibration calculations on entire

unit cells.

It should be emphasised that while this symmetry transformation can be

used for calculations of the normal mode eigenvectors and frequencies

for the zero wavevector it does not hold at other values for all additional

values. Therefore, simple symmetry arguments such as these do not hold

for phonon calculations.

Symmetry can also be used to block the dynamical matrix into several

smaller matrices each corresponding to a different symmetry species,

thereby greatly reducing the time needed for diagonalisation and

automatically helping to identify the normal modes. Symmetry blocking

is not coded at the moment.

References.

Lattice Dynamics of Molecular Crystals", Lecture Notes in Chemistry 26,

S.Califano, V.Schettino and N.Neto (1981), Springer-Verlag, Berlin,

Heidelberg and New York. A comprehensive monograph with good sections

on the theory of lattice vibrations and normal mode symmetries.

A.Warshel and S.Lifson, J.Chem.Phys. (1970), 53, 582. The original CFF

paper on crystal calculations. It describes the theory behind crystal

optimisations and vibrational calculations.

E.Huler and A.Warshel, Acta Cryst. (1974), B30, 1822. An extension of

the work in reference 2.

"Infrared and Raman Spectra of Crystals", G.Turrell (1972), Academic

Press, London and New York. A nice clear introduction to the subject.

Background and Implementation.

The Crystal options and their commands were described above. The present

section discusses relevant background material and briefly reviews the

methods used in the implementation. Some technical points are also made.

The crystal option is an extension to the CHARMM program. The source

code is in the directory [.IMAGE] whilst the crystal data structure is in

the file IMAGE.FCM. Two additional source code files have been added -

CRYSTL.SRC and XTLFRQ.SRC. Small modifications have been made to the

files ENERGY.SRC and EIMAGE.SRC.

CHARMM Images and the Crystal Image Data Structure.

As outlined above a crystal structure can be specified entirely

by the action of the primitive translations A, B and C, and a small set of

transformations, {T} (which themselves are functions of A, B and C), on an

asymmetric group of atoms. In CHARMM the calculation of the energy assumes

that there exists a cutoff distance beyond which all interactions between

particles are neglected so that when performing calculations on

supposedly infinite crystals only a limited portion of that crystal, i.e.

that portion containing those atoms within the cutoff distance of the

primary atoms, need be considered.

The CHARMM image option, of course, already enables the energies of

crystals to be calculated but the input required to use it to do so is

cumbersome and time consuming. It is a great simplification to include an

extra data structure that defines the crystal in terms of A, B and C and

{T}.

There are a number of advantages:

1. A crystal is regular so that its generation can be automated. All that

needs to be done is to systematically transform the primary atoms by

one of the set {T} and a linear combination of A, B and C.

The result is obviously best stored in terms of A, B, and C

rather than as absolute numerical values of the transformations.

2. It is essential to define a CHARMM crystal by A, B and C and {T} if the

lattice parameters a, b, c, alpha, beta and gamma are to be varied

because the coordinates of all the image atoms within the crystal will

change during successive cycles of the optimisation as a, b, c, alpha,

beta and gamma themselves change.

3. When constructing the dynamical matrix for a non-zero wave-vector it is

necessary to know the unit cell to which a particular atom belongs in

order to evaluate the exponential factor in the expression.

Although the crystal data structure and the values of the lattice

parameters define the crystal the individual transformations have to be

worked out explicitly in order to determine energies, harmonic frequencies

and so on. In the present version of the program the IMAGE facility is

used, so that a new set of IMAGE transformations are calculated from the

crystal data structure as soon as a crystal is built or every time the

lattice parameters are changed. The use of the IMAGE facility means that

the number of transformations that can be used is determined by the

dimension of the IMAGE arrays (MAXTRN in DIMENS.FCM).

Crystal and Image Patching, Image H-bonds

Crystal image patching is available in the present version of the

program, so that bonds between images are permitted, but with some

restrictions. The IMPAtch command requires the name of the image

transformation, so one *must* use CRYSTAL READ instead of CRYSTAL

BUILD, in order to preserve the names of the image transformations.

Hydrogen-bond interactions described by an explicit hydrogen-bond function

between primary and image atoms are forbidden.

The Lattice Coordinate System.

WARNING: If your system is not properly rotated, there will usually be

bad contacts. If you have bad contacts, check the alignment.

The convention used by CHARMM for orientating the crystal in real space involves

the use of a symmetric transformation (h) matrix. For non-orthorhombic systems,

these coordinates are different (rotated) from the aligned conventioned used by

PDB and others. The conversion is performed by the COOR CONVert command,

see

**»**corman Syntax.The Structure of the Crystal File.

The crystal file is divided into three parts.

A standard CHARMM title.

A symmetry operation declaration section headed by the word Symmetry

and terminated by an End. The transformations are written in the same

way as for the Crystal Build command except that the identity

transformation has to be explicitly listed.

An image section headed by Images and terminated by an End. Here the

images are defined in terms of the symmetry transformations and the

lattice translations A, B and C. The comment line shows the column

labelling.

Sometimes it is useful to write one's own crystal files without recourse

to the Crystal Build option. In this case the symmetry and image blocks

can be put in any order (although only one of each is allowed) and there

is no restriction on the positioning of blank and comment lines.

Two examples of a crystal file are:

* Crystal file for a P1bar crystal.

Symmetry

(X,Y,Z)

(-X,-Y,-Z)

End

Images

! Operation a b c

1 0 0 -1

1 0 0 1

2 0 0 0

End

* Crystal file for a P212121 crystal.

Symmetry

(X,Y,Z)

(X+1/2,-Y+1/2,-Z)

(-X,Y+1/2,-Z+1/2)

(-X+1/2,-Y,Z+1/2)

End

Images

! Operation a b c

2 0 0 0

3 0 0 0

4 0 0 0

2 -1 0 0

3 0 -1 0

4 0 0 -1

End

Second Derivative Calculations and the Use of Symmetry.

Consider a crystal with a unit cell in which there is more than one

asymmetric unit (i.e. all space groups other than P1). The dynamical

matrix then takes a blocked form, with Z**2 blocks if Z is the number

of asymmetric units. Each block is of dimension 3N x 3N and contains

the sum over all unit cells of the second derivative interaction

elements between the Mth and Nth asymmetric units. It is possible to

calculate only the Z blocks (11), (12), ..., (1M), ..., (1Z) and then

transform them to produce the full matrix. In the present program,

however, it is necessary to perform vibration calculations on entire

unit cells.

It should be emphasised that while this symmetry transformation can be

used for calculations of the normal mode eigenvectors and frequencies

for the zero wavevector it does not hold at other values for all additional

values. Therefore, simple symmetry arguments such as these do not hold

for phonon calculations.

Symmetry can also be used to block the dynamical matrix into several

smaller matrices each corresponding to a different symmetry species,

thereby greatly reducing the time needed for diagonalisation and

automatically helping to identify the normal modes. Symmetry blocking

is not coded at the moment.

References.

Lattice Dynamics of Molecular Crystals", Lecture Notes in Chemistry 26,

S.Califano, V.Schettino and N.Neto (1981), Springer-Verlag, Berlin,

Heidelberg and New York. A comprehensive monograph with good sections

on the theory of lattice vibrations and normal mode symmetries.

A.Warshel and S.Lifson, J.Chem.Phys. (1970), 53, 582. The original CFF

paper on crystal calculations. It describes the theory behind crystal

optimisations and vibrational calculations.

E.Huler and A.Warshel, Acta Cryst. (1974), B30, 1822. An extension of

the work in reference 2.

"Infrared and Raman Spectra of Crystals", G.Turrell (1972), Academic

Press, London and New York. A nice clear introduction to the subject.