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# rxncons (c47b2)

Rxncons: Commands for holonomic constrains of different order parameters

Author: Jhih-Wei Chu, June 30, 2007

Email : jwchu@berkeley.edu

The commands described in this node are associated with the holonomic

constraints of several order parameters that may be used to study the

reactions of biomolecules. Current implementation includes 4 kinds of

order parameters.

1. BDIS, keeps the difference between the lengths of two connected bonds

at the designated value

2. BOND, keeps the distance between two particles at the designated value

3. PCNS, keeps the distances (can be rms best fit distances) of

a structure between two other reference structures equal

4. PATH, keeps the distances (can be rms best fit distances) between replicas

equal to each other, replicas need to be generated by using

the replica command first, » replica to replicate a system

into many copies.

* Syntax | Syntax of the rxncons commands

* Usage | Description of command usage

* Implementation | A brief description of the anatomy of RCONstraint

* Restrictions | Restrictions on usage

* Examples | Supplementary examples of the use of RCONstraint

Author: Jhih-Wei Chu, June 30, 2007

Email : jwchu@berkeley.edu

The commands described in this node are associated with the holonomic

constraints of several order parameters that may be used to study the

reactions of biomolecules. Current implementation includes 4 kinds of

order parameters.

1. BDIS, keeps the difference between the lengths of two connected bonds

at the designated value

2. BOND, keeps the distance between two particles at the designated value

3. PCNS, keeps the distances (can be rms best fit distances) of

a structure between two other reference structures equal

4. PATH, keeps the distances (can be rms best fit distances) between replicas

equal to each other, replicas need to be generated by using

the replica command first, » replica to replicate a system

into many copies.

* Syntax | Syntax of the rxncons commands

* Usage | Description of command usage

* Implementation | A brief description of the anatomy of RCONstraint

* Restrictions | Restrictions on usage

* Examples | Supplementary examples of the use of RCONstraint

Top

Syntax of RCONstaint commands

[SYNTAX: RCONstaint commands]

RCONstraint { [BDIS repeat(3x(atom-spec)) ] [RXNC real] [PLAG] -

[IUNL integer] [MAXIter integer] }

{ [BOND repeat(2x(atom-spec)) ] [RXNC real] [PLAG] -

[IUNL integer] [MAXIter integer] }

{ [PCNS] [RXNC real] [PLAG] -

[IUNL integer] [MAXIter integer] }

{ [NOTRanslation] [NOROtation] -

[MASS] [WEIG] [MAXIter integer] }

{ [PATH] [PLAG] [IUNL integer] [MAXIter integer] }

{ [CYCLic] [NOTRanslation] [NOROtation] -

[MASS] [WEIG] [MAXIter integer] }

{ [CLEAn] [type] }

Keyword Purpose

BIDS Keeps the difference between the lengths of two connected bonds

at the designated value

BOND Keeps the distance between two particles at the designated value.

PCNS Keeps the distances (can be rms best fit distances) of

a structure between two other reference structures equal.

One of the refernce structure will be read from the COMP array,

and the other will be read from the REF array. The scalar command

may be used to copy coordinates to these arrays. Also see the

examples.

PATH Keeps the distances (can be rms best fit distances) between replicas

equal to each other, replicas need to be generated by using the

replica command first, » replica to replica a system to many

copies.

RXNC The value of the constraned order parameter.

The default value is 0.0 for BDIS.

Negative or zero value will cause error in BOND.

PLAG Flag to active the output of the lagrange multipliers that are

requires to satisfy the constraint during a dynamic simulation

(dynamc.src).

In addition, the Z and G factors as defined in Sprik M, Ciccotti G

"Free energy from constrained molecular dynamics"

JOURNAL OF CHEMICAL PHYSICS 109 (18): 7737-7744 NOV 8 1998

will also be recorded in PLAG is specificed.

IUNL Unit for outputing the lagrange multiplers. Frequency of the output

is NSACC (» dynamc ).

MAXI Maximium allowable steps of iterations for solving the nonlinear

algebraic equation(s) of the constraint.

CYCL Specifies that a path is cyclic

NOTR Calculate the distances between replicas WITHOUT overlaying their

centers.

NORO Calculate the distances between replicas WITHOUT doing rotational

best fit

MASS Use mass weighted distance.

WEIG Use wmain array to weight the atoms of each replica.

CLEA Clean up the pointers of the constraints. Should be called after

RCONS is no longer used.

atom-spec:== (see

Syntax of RCONstaint commands

[SYNTAX: RCONstaint commands]

RCONstraint { [BDIS repeat(3x(atom-spec)) ] [RXNC real] [PLAG] -

[IUNL integer] [MAXIter integer] }

{ [BOND repeat(2x(atom-spec)) ] [RXNC real] [PLAG] -

[IUNL integer] [MAXIter integer] }

{ [PCNS] [RXNC real] [PLAG] -

[IUNL integer] [MAXIter integer] }

{ [NOTRanslation] [NOROtation] -

[MASS] [WEIG] [MAXIter integer] }

{ [PATH] [PLAG] [IUNL integer] [MAXIter integer] }

{ [CYCLic] [NOTRanslation] [NOROtation] -

[MASS] [WEIG] [MAXIter integer] }

{ [CLEAn] [type] }

Keyword Purpose

BIDS Keeps the difference between the lengths of two connected bonds

at the designated value

BOND Keeps the distance between two particles at the designated value.

PCNS Keeps the distances (can be rms best fit distances) of

a structure between two other reference structures equal.

One of the refernce structure will be read from the COMP array,

and the other will be read from the REF array. The scalar command

may be used to copy coordinates to these arrays. Also see the

examples.

PATH Keeps the distances (can be rms best fit distances) between replicas

equal to each other, replicas need to be generated by using the

replica command first, » replica to replica a system to many

copies.

RXNC The value of the constraned order parameter.

The default value is 0.0 for BDIS.

Negative or zero value will cause error in BOND.

PLAG Flag to active the output of the lagrange multipliers that are

requires to satisfy the constraint during a dynamic simulation

(dynamc.src).

In addition, the Z and G factors as defined in Sprik M, Ciccotti G

"Free energy from constrained molecular dynamics"

JOURNAL OF CHEMICAL PHYSICS 109 (18): 7737-7744 NOV 8 1998

will also be recorded in PLAG is specificed.

IUNL Unit for outputing the lagrange multiplers. Frequency of the output

is NSACC (» dynamc ).

MAXI Maximium allowable steps of iterations for solving the nonlinear

algebraic equation(s) of the constraint.

CYCL Specifies that a path is cyclic

NOTR Calculate the distances between replicas WITHOUT overlaying their

centers.

NORO Calculate the distances between replicas WITHOUT doing rotational

best fit

MASS Use mass weighted distance.

WEIG Use wmain array to weight the atoms of each replica.

CLEA Clean up the pointers of the constraints. Should be called after

RCONS is no longer used.

atom-spec:== (see

**»**select )Top

Description of RCONStraint command usage

This command treats ONE selected reaction coordinate (order parameter) as a

holonomic constraint. Currently, only one reaction coordinate is allowed.

Generalization to multiplie reaction coordinates will be implemented in the

future.

This command is included as part of the holonomic constraints that are

involved in CHARMM, such as SHAKE, LONEpair, etc. In other words,

the subroutines of RCON are called from HOLONOM.SRC

The BDIS constraint fixes the difference between two connected bonds at

the value specified to RXNC. Only THREE atoms are allowed to be chosen,

since the two bonds are connected.

The BOND constraint fixes the distance between two particles at the value

(must be positive) specified to RXNC.

The PCNS constraint keeps the distances (can be rms best fit distances)

of a structure between two other reference structures equal. This constraint

can be used to sample the configuration space on the hyperplane that is

in the middle between two reference structures. The reference structures may

be obtained by different methods, such as the replica/path or nudeged

elastic band method (» replica ). The averaged forces that are required

to maintain the constraints of this type along a reference path can be used

to compute the potential of mean force along this path.

The PATH constraint keeps the distances (can be rms best fit distances)

between replicas equal to each other, replicas need to be generated by using

the replica command first, » replica to replica a system into many

copies. This constraint is able to avoid the sliding down and corner-cutting

problems of the replica/path method without doing force projections as in

nudged elastic band or the string methods, and the results are thus more

reliable.

Description of RCONStraint command usage

This command treats ONE selected reaction coordinate (order parameter) as a

holonomic constraint. Currently, only one reaction coordinate is allowed.

Generalization to multiplie reaction coordinates will be implemented in the

future.

This command is included as part of the holonomic constraints that are

involved in CHARMM, such as SHAKE, LONEpair, etc. In other words,

the subroutines of RCON are called from HOLONOM.SRC

The BDIS constraint fixes the difference between two connected bonds at

the value specified to RXNC. Only THREE atoms are allowed to be chosen,

since the two bonds are connected.

The BOND constraint fixes the distance between two particles at the value

(must be positive) specified to RXNC.

The PCNS constraint keeps the distances (can be rms best fit distances)

of a structure between two other reference structures equal. This constraint

can be used to sample the configuration space on the hyperplane that is

in the middle between two reference structures. The reference structures may

be obtained by different methods, such as the replica/path or nudeged

elastic band method (» replica ). The averaged forces that are required

to maintain the constraints of this type along a reference path can be used

to compute the potential of mean force along this path.

The PATH constraint keeps the distances (can be rms best fit distances)

between replicas equal to each other, replicas need to be generated by using

the replica command first, » replica to replica a system into many

copies. This constraint is able to avoid the sliding down and corner-cutting

problems of the replica/path method without doing force projections as in

nudged elastic band or the string methods, and the results are thus more

reliable.

Top

Restrictions

The holonomic constraints in CHARMM are not fully integrated and there may be

problems if all types of holonomic constraints are present. This needs to be

fixed.

Only one reaction coordinate is allowed in the current implementation.

Generalization to multiple reaction coordinates is under development.

Other types of order parameters may be implemented. Seggestions are welcome;

please send suggestions to jwchu@berkeley.edu

No lagrange multipliers will be output for the PATH constraint. It is not

recommended to run dynamics with the PATH constraint at this point.

Restrictions

The holonomic constraints in CHARMM are not fully integrated and there may be

problems if all types of holonomic constraints are present. This needs to be

fixed.

Only one reaction coordinate is allowed in the current implementation.

Generalization to multiple reaction coordinates is under development.

Other types of order parameters may be implemented. Seggestions are welcome;

please send suggestions to jwchu@berkeley.edu

No lagrange multipliers will be output for the PATH constraint. It is not

recommended to run dynamics with the PATH constraint at this point.

Top

Supplementary examples.

1. The BDIS constraint

RCON BDIS rxnc 0.0 sele bynu 8 end sele bynu 3 .or. bynu 11 end iunl 66

will keep ( distance between atom 8 and 3 ) - ( distance between 3 and 11 )

at 0.0 lagrange multiplers will be output to file with unit 66

2. The bond constraint

RCON BOND plag rxnc 11.0 sele bynu 3 end sele bynu 11 end iunl 66

will keep the distance between atom 3 and 11 at the value of 11.0 A.

lagrange multiplers will be output to file with unit 66

3. The plane constraint

open read card unit 44 name a.crd

read coor unit 44 ignore comp

close unit 44

scalar xref = xcomp

scalar yref = ycomp

scalar zref = zcomp

open read card unit 44 name b.crd

read coor unit 44 ignore comp

close unit 44

RCON PCNS rxnc 0.0 plag weig iunl 66

will keep the system at the same distance to a.crd and to b.crd

the weighting array will be used to calcualte the weighted distance

lgrange multiplers will be output to file with unit 66

4. The reaction path constratint

RCON PATH rxnc 0.0 plag cycl mass

will keep the distances between the replicas of a cyclic path equal.

The distances will be mass weighted.

See also

rxncons.inp

rxncons_rpath.inp

Supplementary examples.

1. The BDIS constraint

RCON BDIS rxnc 0.0 sele bynu 8 end sele bynu 3 .or. bynu 11 end iunl 66

will keep ( distance between atom 8 and 3 ) - ( distance between 3 and 11 )

at 0.0 lagrange multiplers will be output to file with unit 66

2. The bond constraint

RCON BOND plag rxnc 11.0 sele bynu 3 end sele bynu 11 end iunl 66

will keep the distance between atom 3 and 11 at the value of 11.0 A.

lagrange multiplers will be output to file with unit 66

3. The plane constraint

open read card unit 44 name a.crd

read coor unit 44 ignore comp

close unit 44

scalar xref = xcomp

scalar yref = ycomp

scalar zref = zcomp

open read card unit 44 name b.crd

read coor unit 44 ignore comp

close unit 44

RCON PCNS rxnc 0.0 plag weig iunl 66

will keep the system at the same distance to a.crd and to b.crd

the weighting array will be used to calcualte the weighted distance

lgrange multiplers will be output to file with unit 66

4. The reaction path constratint

RCON PATH rxnc 0.0 plag cycl mass

will keep the distances between the replicas of a cyclic path equal.

The distances will be mass weighted.

See also

rxncons.inp

rxncons_rpath.inp