# rdfsol (c47b2)

Radial Correlation Functions

The RDFSOL command computes radially resolved correlation

functions, such as radial distribution functions or orientational

correlation functions. The function of interest is computed either between

pairs of atoms from two atom selections, or between a pair consisting of

one atom selection and a reference point, which can be either a fixed point

in space or the center of mass of a set of atoms. As the name rdfSOL

suggests, the routine allows for the special treatment of solvent molecules

(TIP3 water is supported by special routines, others need the use of the

PROTotype facility (see

* Syntax | The syntax of the RDFSOL command

* General | General overview

* Sets | Set selections

* Limit | Locally limiting sets in each frame

* Options | other general options

* Traj | Trajectory specifications

* Caveats | Some limitations/todos to keep in mind

* Examples | Just what it says

The RDFSOL command computes radially resolved correlation

functions, such as radial distribution functions or orientational

correlation functions. The function of interest is computed either between

pairs of atoms from two atom selections, or between a pair consisting of

one atom selection and a reference point, which can be either a fixed point

in space or the center of mass of a set of atoms. As the name rdfSOL

suggests, the routine allows for the special treatment of solvent molecules

(TIP3 water is supported by special routines, others need the use of the

PROTotype facility (see

**»**proto )).* Syntax | The syntax of the RDFSOL command

* General | General overview

* Sets | Set selections

* Limit | Locally limiting sets in each frame

* Options | other general options

* Traj | Trajectory specifications

* Caveats | Some limitations/todos to keep in mind

* Examples | Just what it says

Top

Syntax for the RDFSOL command

[SYNTAX RadialDistributionFunctions_with_SOLvent]

Syntax:

RDFSOL [ RDF int ] [ DDIP int ] [ QDIP int ] [ HD int ] -

[ setA-spec ] [ setB-spec ] [ around-spec ] -

[ SAME ] [ RMAX real ] [ NBIN int ] -

[ VOLUme real ] [ PRECise ] [ BRUTe ] [ MINI ] -

[ traj-spec ] [ SPFAc int]

setA-spec:: [ SITE ] [ atom-selection ]

[ XREF real ] [ YREF real ] [ ZREF real ]

[ WATEr ]

[ PROTo int ]

setB-spec:: [ SITE ] [ atom-selection ]

[ WATEr ]

[ PROTo int ]

around-spec:: AROUnd [ RAROund real ] [ LOCAl ] -

[ atom-selection ]

[ XREF real ] [ YREF real ] [ ZREF real ]

traj-spec:: [ FIRStu int ] [ NUNIt int ] [ BEGIn int ] -

[ STOP int ] [ SKIP int ] [ RPICo | TSET real ]

atom-selection::= see

Syntax for the RDFSOL command

[SYNTAX RadialDistributionFunctions_with_SOLvent]

Syntax:

RDFSOL [ RDF int ] [ DDIP int ] [ QDIP int ] [ HD int ] -

[ setA-spec ] [ setB-spec ] [ around-spec ] -

[ SAME ] [ RMAX real ] [ NBIN int ] -

[ VOLUme real ] [ PRECise ] [ BRUTe ] [ MINI ] -

[ traj-spec ] [ SPFAc int]

setA-spec:: [ SITE ] [ atom-selection ]

[ XREF real ] [ YREF real ] [ ZREF real ]

[ WATEr ]

[ PROTo int ]

setB-spec:: [ SITE ] [ atom-selection ]

[ WATEr ]

[ PROTo int ]

around-spec:: AROUnd [ RAROund real ] [ LOCAl ] -

[ atom-selection ]

[ XREF real ] [ YREF real ] [ ZREF real ]

traj-spec:: [ FIRStu int ] [ NUNIt int ] [ BEGIn int ] -

[ STOP int ] [ SKIP int ] [ RPICo | TSET real ]

atom-selection::= see

**»**selectTop

General overview and options

RDFSOL calculates radially resolved pair-distribution or angular

correlation functions between two sets of atoms (setA and setB).

The type of function computed is selected by keywords:

RDF - Radial Distribution Function

If one of the two sets is WATEr then distribution functions

for the oxygen and hydrogens are computed.

If both sets are WATEr then the hydrogen-hydrogen distribution

function will also be evaluated.

If the first set is not water and the keyword SITE is present,

the center of mass of the set is taken as single center. Else

the average over all points in setA is taken.

DDIP - Dipole-Dipole correlation function. If one or both sets are

not WATEr the center of mass and dipole moment of this set

is used (no matter whether the keyword SITE is present or

not). In this case setA must not be a fixed point in space

since the dipole moment is not defined in this case.

QDIP - Charge-Dipole correlation function. As with RDF setA can

either be a SITE or the average of all points.

The integer after each function to be calculated gives the unit number

the respective function is to be written to.

General overview and options

RDFSOL calculates radially resolved pair-distribution or angular

correlation functions between two sets of atoms (setA and setB).

The type of function computed is selected by keywords:

RDF - Radial Distribution Function

If one of the two sets is WATEr then distribution functions

for the oxygen and hydrogens are computed.

If both sets are WATEr then the hydrogen-hydrogen distribution

function will also be evaluated.

If the first set is not water and the keyword SITE is present,

the center of mass of the set is taken as single center. Else

the average over all points in setA is taken.

DDIP - Dipole-Dipole correlation function. If one or both sets are

not WATEr the center of mass and dipole moment of this set

is used (no matter whether the keyword SITE is present or

not). In this case setA must not be a fixed point in space

since the dipole moment is not defined in this case.

QDIP - Charge-Dipole correlation function. As with RDF setA can

either be a SITE or the average of all points.

The integer after each function to be calculated gives the unit number

the respective function is to be written to.

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SiteA/B specifications

SetA and SetB are two sets for which the chosen function is evaluated

for all pairs A-B. Both can be WATEr, in which all TIP3 residues present

will be included. In this case the oxygen positions will be used as the

centers of the molecules. In both cases the center of mass (and set

dipole moment if needed) can be used if the keyword SITE is present.

SetA can be a fixed point in space: (XREF/YREF/ZREF) (if SITE is present

but no atom selection (0/0/0) will be used as default).

Finally for each of the two sets a previously defined prototype set

(see

the center of geometry (or mass with keyword MASS) and dipole of each

individual set member will be used in the requested functions.

For both sets WATEr is the default.

SiteA/B specifications

SetA and SetB are two sets for which the chosen function is evaluated

for all pairs A-B. Both can be WATEr, in which all TIP3 residues present

will be included. In this case the oxygen positions will be used as the

centers of the molecules. In both cases the center of mass (and set

dipole moment if needed) can be used if the keyword SITE is present.

SetA can be a fixed point in space: (XREF/YREF/ZREF) (if SITE is present

but no atom selection (0/0/0) will be used as default).

Finally for each of the two sets a previously defined prototype set

(see

**»**proto ) can be used. In this casethe center of geometry (or mass with keyword MASS) and dipole of each

individual set member will be used in the requested functions.

For both sets WATEr is the default.

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Limiting Sets

If only a subset which is localized around a certain point should be

used in each frame this can be achieved by the AROUnd keyword. If it is

present setA will be re-selected in each frame. If the keyword LOCAl is

present setB will also be re-selected. RAROund <real> is the radius

around the selected center within which an atom must lie to be available

for evaluation in this frame. The center itself can either be a fixed

point in space (XREF/YREF/ZREF) or an atom selection of which the center

of mass will be used.

Limiting Sets

If only a subset which is localized around a certain point should be

used in each frame this can be achieved by the AROUnd keyword. If it is

present setA will be re-selected in each frame. If the keyword LOCAl is

present setB will also be re-selected. RAROund <real> is the radius

around the selected center within which an atom must lie to be available

for evaluation in this frame. The center itself can either be a fixed

point in space (XREF/YREF/ZREF) or an atom selection of which the center

of mass will be used.

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Other options

----------------------------------------------------------------------

SAME - if this keyword is present, only setA is used for both

sets, thus calculating auto-functions (this algorithm

should be faster than the general one if setA and setB

use the same selection)

----------------------------------------------------------------------

RMAX <real> - the maximum distance up to which a pair A-B is evaluated

(default: 7.5A)

----------------------------------------------------------------------

NBIN <int> - the number of bins used to sample (each bin is RMAX/NBIN

wide)

(default: 150)

----------------------------------------------------------------------

VOLUme <real> - the volume of the total system, necessary for the

normalization. If not specified by the user and crystal

is in use, the resulting cell volume will be used.

Finally, if crystal is not used and no volume

is specified, and if both sets are localized (see AROUnd),

the volume of the limiting sphere will be used.

----------------------------------------------------------------------

PRECise - if RDFs are calculated and one or both sets contain

WATEr, some pairs including water hydrogens will be

missed since only oxygen distances are evaluated.

If PRECise is present, these pairs are also included

which results in a slightly diminished efficiency of the

cubing algorithm

----------------------------------------------------------------------

BRUTe - use a simple double loop algorithm rather than a cubing

algorithm

----------------------------------------------------------------------

MINI - use 'real' minimum image conventions. Currently only one

function can be calculated if MINI is used. Its major use

is the computation of the distance dependent Kirkwood

G-factor (with DDIP, second column). Here, one needs to go

'into the corners' (i.e. sqrt(3)/2 * L for a cubic box)

without counting pairs twice.

(caution: needs lots of memory)

----------------------------------------------------------------------

SPFAc - if images are present, the number of total

atoms/pairs/cubes may change from frame to frame.

So an estimate of the needed space needs to be made

before reading the trajectory so SPFAc times the actual

values is allocated

(default: 3)

----------------------------------------------------------------------

Other options

----------------------------------------------------------------------

SAME - if this keyword is present, only setA is used for both

sets, thus calculating auto-functions (this algorithm

should be faster than the general one if setA and setB

use the same selection)

----------------------------------------------------------------------

RMAX <real> - the maximum distance up to which a pair A-B is evaluated

(default: 7.5A)

----------------------------------------------------------------------

NBIN <int> - the number of bins used to sample (each bin is RMAX/NBIN

wide)

(default: 150)

----------------------------------------------------------------------

VOLUme <real> - the volume of the total system, necessary for the

normalization. If not specified by the user and crystal

is in use, the resulting cell volume will be used.

Finally, if crystal is not used and no volume

is specified, and if both sets are localized (see AROUnd),

the volume of the limiting sphere will be used.

----------------------------------------------------------------------

PRECise - if RDFs are calculated and one or both sets contain

WATEr, some pairs including water hydrogens will be

missed since only oxygen distances are evaluated.

If PRECise is present, these pairs are also included

which results in a slightly diminished efficiency of the

cubing algorithm

----------------------------------------------------------------------

BRUTe - use a simple double loop algorithm rather than a cubing

algorithm

----------------------------------------------------------------------

MINI - use 'real' minimum image conventions. Currently only one

function can be calculated if MINI is used. Its major use

is the computation of the distance dependent Kirkwood

G-factor (with DDIP, second column). Here, one needs to go

'into the corners' (i.e. sqrt(3)/2 * L for a cubic box)

without counting pairs twice.

(caution: needs lots of memory)

----------------------------------------------------------------------

SPFAc - if images are present, the number of total

atoms/pairs/cubes may change from frame to frame.

So an estimate of the needed space needs to be made

before reading the trajectory so SPFAc times the actual

values is allocated

(default: 3)

----------------------------------------------------------------------

Top

Trajectory specifications

These are the usual specs. The trajectory is read NUNIt units starting

with FIRSTu reading from frame BEGIn to STOP where SKIP frames are

skipped between reading.

These additional keywords influence the reading and writing of the timestep

field (DELTA), useful when importing trajectories (DCD files) from external

sources that may not set this value correctly in AKMA time units.

TSET real Overrride the value in the file with this value (picoseconds)

RPICo Flag; convert file value to AKMA; assumes value is in picoseconds

Trajectory specifications

These are the usual specs. The trajectory is read NUNIt units starting

with FIRSTu reading from frame BEGIn to STOP where SKIP frames are

skipped between reading.

These additional keywords influence the reading and writing of the timestep

field (DELTA), useful when importing trajectories (DCD files) from external

sources that may not set this value correctly in AKMA time units.

TSET real Overrride the value in the file with this value (picoseconds)

RPICo Flag; convert file value to AKMA; assumes value is in picoseconds

Top

Caveats and Comments

- When computing dipole-dipole correlations for a set which is not WATEr,

only its center of mass and dipole moment for primary atoms will be

evaluated. So if a part of a large molecule which is re-centered

bysegment (e.g. a protein) and "sticks out" of the primary box, some

pairs may not be sampled.

- Normalization of RDFs differs slightly from that used in COOR ANAL

- no excluded volume correction

- point-point (e.g. two SITEs or DDIP for two non-WATEr sets...) not yet

implemented

Caveats and Comments

- When computing dipole-dipole correlations for a set which is not WATEr,

only its center of mass and dipole moment for primary atoms will be

evaluated. So if a part of a large molecule which is re-centered

bysegment (e.g. a protein) and "sticks out" of the primary box, some

pairs may not be sampled.

- Normalization of RDFs differs slightly from that used in COOR ANAL

- no excluded volume correction

- point-point (e.g. two SITEs or DDIP for two non-WATEr sets...) not yet

implemented

Top

Examples

(See also test/c30test/rdfsol.inp test/c30test/rdfsol2.inp testcases)

----------------------------------------------------------------------

RDFSOL RDF 10 SETA WATER SAME RMAX 7.5 NBIN 150 PRECISE -

FIRSTUNIT 11 NUNIT 1

This will calculate g_OO, g_OH and g_HH for all waters in the simulated

system up to 7.5 A into 150 bins. One trajectory file will be read from

unit 11 and the result output to unit 10.

----------------------------------------------------------------------

RDFSOL RDF 10 SETA WATER SAME RMAX 7.5 NBIN 150 PRECISE -

AROUND RAROUND 7.5 LOCAL SELECT ATOM PROT 1 NH END -

FIRSTUNIT 11 NUNIT 1

The same as above but only waters around the NH of residue 1 of segment

PROT will be considered.

----------------------------------------------------------------------

RDFSOL RDF 10 QDIP 11 DDIP 12 SETA WATER SAME RMAX 7.5 NBIN 150 PRECISE -

FIRSTUNIT 13 NUNIT 1

Same sets as in the first example but here all three functions are

calculated at once (i.e. the trajectory is only read once).

----------------------------------------------------------------------

Examples

(See also test/c30test/rdfsol.inp test/c30test/rdfsol2.inp testcases)

----------------------------------------------------------------------

RDFSOL RDF 10 SETA WATER SAME RMAX 7.5 NBIN 150 PRECISE -

FIRSTUNIT 11 NUNIT 1

This will calculate g_OO, g_OH and g_HH for all waters in the simulated

system up to 7.5 A into 150 bins. One trajectory file will be read from

unit 11 and the result output to unit 10.

----------------------------------------------------------------------

RDFSOL RDF 10 SETA WATER SAME RMAX 7.5 NBIN 150 PRECISE -

AROUND RAROUND 7.5 LOCAL SELECT ATOM PROT 1 NH END -

FIRSTUNIT 11 NUNIT 1

The same as above but only waters around the NH of residue 1 of segment

PROT will be considered.

----------------------------------------------------------------------

RDFSOL RDF 10 QDIP 11 DDIP 12 SETA WATER SAME RMAX 7.5 NBIN 150 PRECISE -

FIRSTUNIT 13 NUNIT 1

Same sets as in the first example but here all three functions are

calculated at once (i.e. the trajectory is only read once).

----------------------------------------------------------------------