Solvent Correlation Functions
CORSOL is inspired by the CORREL module and serves the compute
(solvent-related) correlation functions. The difference between the
two modules is that CORSOL is designed to calculate correlation
functions for many atoms/groups/molecules simultaneously but to return only the
sum/average of the individual correlation functions. This would be tedious to
achieve with CORREL since it would require the entering of
many (think of the typical number of water molecules in a solution
study) identical CORREL series. Further, CORREL calculates the
correlation functions only after the underlying time series has been
accumulated. Thus, the calculation of summed/averaged correlation
functions would either be limited to short time series or require to
break up the problem into multiple processing sweeps over
the same trajectorie(s).
While correlation functions in CORSOL can be computed by FFT
after the complete acquisition for short series, the default mode of
operation is to keep only a certain number of datapoints and to calculate the
correlation functions after each addition of a datapoint by a rotating
window algorithm. While this method is much more costly
calculation-wise - and thus considerably slower - than the
FFT-method, it has the advantage that the amount of memory required depends
only on the number of atoms considered and the length
requested for a particular correlation function (instead of the length of
the full time-series!). Thus, even slowly converging properties,
which require the analysis of long trajectories, can be handled in "one
go" provided that not too man datapoints are requested for the final function.
* Syntax / The syntax of the correlation command
* General / General information regarding the correlation section
* Enter / How to specify time series
* Trajectory / How to reference to trajectory files
* IO / Input/output guide to correlation functions and series
* Examples / Just what it says
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Syntax for the CORSOL command and subcommands
[SYNTAX CORrelate SOLvent]
Syntax:
CORSOL [ MAXTimesteps int ] [ MAXSeries int ] [ MAXAtoms ] -
default 512 default 2 default 100
[ nonbond-spec ] [ hbond-spec ] [ image-spec ] [NOUPdate]
[ INBFrq 0 ] [ IHBFrq 0 ] [ IMGFrq 0 ]
hbond-spec Hbonds .
nonbond-spec Nbonds .
image-spec Images Update.
Subcommands:
ENTEr name { [ DDIP repeat(2x(atom-spec)) ] global-spec } c
{ [ WREO atom-spec ] [ NORM ] [ P2 ] global-spec } c
{ [ VACF atom-spec ] [ CHARge ] global-spec } v
{ [ SATM ] [ SHEL int ] atom-spec global-spec } c*
{ [ BULK ] }
{ }
{ [ SATX ] [ SHL1 int ] [ SHL2 int ] atom-spec global-spec } c*
{ [ BULK ] [ BULK ] }
{ }
{ [ MRTI ] [ SHEL int ] atom-spec global-spec } c*
{ [ BULK ] }
{ }
( code: c-coordinates, v-velocities, e-either )
atom-spec::= { SELE atom-selection END}
global-spec::= all series support the following options:
[ FFT ] or [ NCORr int ]
[ IMAX unit-nr ] [ NMAX int ]
* needs a CHARMM executable with SHELL functionality
see Shell
TRAJectory [ FIRStu int ] [ NUNIt int ] [ BEGIn int ] [ STOP int ]
[ SKIP int ] [ VELOcity ] [first-atom-selection]
[ ORIEnt [MASS] second-atom-selection ]
SHOW { ALL } [P2] [UNIT int]
{ time-series-name }
EDIT { ALL }
{ time-series-name } edit-spec
edit-spec::= [INDEx int] [VECCod int] [CLASs int] [SECOnd int]
[TOTAl int] [SKIP int] [DELTa real]
[VALUe real] [NAME new-name] [OFFSet real]
READ { time-series-name } unit-spec edit-spec { [FILE] }
{ CARD }
{ DUMB [COLUmn int] }
WRITe { ALL } { [FILE] }
WRITe { time-series-name } unit-spec { CARD }
{ PLOT }
{ DUMB [ TIME ] }
END ! return to main command parser
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General discussion regarding time series and correlation functions
Discussion:
The CORSOL command invokes the CORSOL subcommand parser. The
keyword values MAXTimesteps, MAXSeries, and MAXAtoms may be specified
for space allocation greater than the default options.
The MAXTimesteps value is the largest number of steps which
will be kept for any series. The MAXSeries keyword is the largest
number of timeseries that will be kept at any time within CORSOL
(NOTE: A 'series' in this context is the resulting correlation
function. I.e. if a function involving 10.000 solvent molecules is to
be calculated, this implies only one 'series' with respect to
MAXT). The MAXAtoms keyword allocates space for the atoms that are
specified in the ENTER commands (also duplicating a time series
requires more space for atoms).
The individual correlation functions to be computed are defined
by the ENTEr command.
The TRAJectory command processes the specified trajectory
file(s). All defined functions are calculated. Here, multiple time
series are kept in memory for each resulting function. After all files
have been processed, the sum/average of all individual (single
atom/group) correlation functions is calculated and stored as the
final result of this 'series'.
The EDIT command allows the user to directly modify the time
series specifications.
The SHOW command will display the specification data for all
of the time series.
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Specifying time series
The ENTER command defines a new series. Each series specified
by different enter commands must have a unique name (up to 4
characters). With this command, a series may be defined and then must
be later filled with a TRAJectory command (or a READ series
command).
The time series names "ALL" may not be used, and are reserved
for selecting all of the time series.
Global options common to all series are:
[ FFT ] - if FFT should be used to calculate the single atom/group
correlation functions rather than the windowing algorithm
(requires enough memory to keep all time-series in memory
simultaneously)
[ NCOR int ] - the number of datapoints to be kept if the windowing
algorithm is to be used. The default is MAXTimesteps.
[ IMAX unit-nr ] - a unit to which the maximum contributions to a single
correlation function are written
[ NMAX int ] - the number of maximum contributions which are to be
written to IMAX
The ENTER options are;
-----------------------------------------------------------------------------
DDIP repeat(2x(atom-spec))
This function calculates the dipole-dipole correlation between
two atoms. The first atom-spec gives a set of atoms (e.g. hydrogen
atoms of a protein). The second set are typically atoms from solvent
molecules (e.g. all protons in the surrounding water). Then the
cumulative dipole-dipole correlation of all atoms in the second
selection to each individual atom in the first selection will be
calculated. Finally the results for all atoms in the first selection
are summed up and this constitutes the final result.
This series will take up 3 result-series (MAXSer at least 3):
the complete function as well radial and angular portion separately.
-----------------------------------------------------------------------------
WREO atom-spec [ NORM ] [ P2 ]
This will calculate the average of the water single-molecule
dipole auto-correlation series. All atoms in the atom-spec are
expected to be TIP3 OH2 (i.e. oxygen) atoms. If NORM is specified the
normalized dipole moments will be used in the calculation. With P2 the
second Legendre polynomial is calculated.
-----------------------------------------------------------------------------
VACF atom-spec
Calculates the average velocity auto-correlation function for
all specified atoms. If the keyword CHARge is present, each datapoint
will be multiplied with the charge of the respective atom, thus,
effectively yielding the flux.
The result uses two series where the second series holds the integral
of the VACF.
-----------------------------------------------------------------------------
SATM [ SHEL int ] atom-spec
[ BULK ]
Enters a series analogous to the CORRel SATM series. For each
atom specified its presence in the specified shell (NOTE: SHELL must
be set up before CORSOL is called, see *note
reorient:(chmdoc/shell.doc)) will be recorded. The resulting
correlation function is the sum of the auto-correlation function for
each specified atom. This resulting function can be used in the
determination of the mean residence time of atoms in a given shell.
-----------------------------------------------------------------------------
SATX [ SHL1 int ] [ SHL2 int ] atom-spec
[ BULK ] [ BULK ]
This ENTER command will yield sum of the cross-correlation
functions of two SATM series for all selected atoms (again, SHELL must
be set up before entering CORSOL).
-----------------------------------------------------------------------------
MRTI [ SHEL int ] atom-spec
[ BULK ]
MRTI offers the means to calculate an alternative definition
of the mean residence time of an atom in a certain SHELL (which,
again, needs to be set up prior to CORSOL). This series differs from
all other series, insofar as it does not calculate correlation
functions but rather produces a histogram. Here for each selected atom
the number of times it has spent a given number of consecutive steps
in the selected SHELL is recorded. Thus, each time an atom leaves this
shell it 'forgets' this 'episode' and will start the step-count again
when it reenters the SHELL. This lack of history yields a different
mean residence time than calculated by the SATM series. (Especially
for atom in the vicinity of the shell boundary, smaller residence
times are more abundant as the atom fluctuates across the SHELL
boundary back and forth).
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Specification of the Trajectory Files
The TRAJectory command reads a number of trajectory files whose
Fortran unit numbers are specified sequentially. The first unit is given
by the FIRSTU keyword and must be specified. NUNIT gives the number of
units to be scanned, and defaults to 1.
BEGIN, STOP, and SKIP are used to specify which steps in the
trajectory are actually used. BEGIN specifies the first step number to
be used. STOP specifies the last. SKIP is used to select steps
periodically as follows: only those steps whose step number is evenly
divisible by STEP are selected. The default value for BEGIN is the first
step in the trajectory; for STOP, it is the last step in the trajectory;
and for SKIP, the default is 1.
If VELOcity is specified, a velocity trajectory will be looked
for. Otherwise, a coordinate trajectory is expected.
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Input/Output of correlation functions.
1) The SHOW command
SHOW { ALL }
{ time-series-name }
The SHOW command displays to print unit various data regarding
the specified time series. This command is automatically run after the
ENTER and EDIT commands as a verification of the last action.
2) The READ command
READ { time-series-name } unit-spec edit-spec { [FILE] }
{ CARD }
{ DUMB [COLUmn int] }
The READ command allows a time series or correlation function to be
directly read. Currently this option is not of great use since no
post-processing of the generated correlation functions is supported.
3) The WRITe command
WRITe { ALL } { [FILE] }
{ time-series-name } unit-spec { CARD }
{ PLOT }
{ DUMB [ TIME ] }
The WRITe command will write out time series or a correlation function.
All of the write options expect a title to follow this command.
There are several file formats; FILE (default), CARD, PLOT, and DUMB.
The FILE and CARD options will write out all data regarding the specified
time series with the expectation for later retrieval by Charmm or another
program. The PLOT option will create a BINARY file for plotting by PLT2.
The first line of the title is used as the plot title, but this may be
reset in PLT2.
The DUMB options will simply write out the values with no title
or header to a card file, one value to a line. If the TIME option is
specified, the time value will precede the time series values (as needed
for an X-Y plot).
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Examples
These examples are meant to be a partial guide in setting up
input files for CORSOL.
Example 1: auto-reorientation function for all waters
CORSOL MAXSERIES 1 MAXTIMESTEPS 500 MAXATOMS 10000
ENTER AAAA WREO NORM SELECT ATOM WAT * OH2 END
TRAJECTORY FIRSTU 51 NUNIT 5
WRITE AAAA UNIT 20 DUMB TIME
* title
END
Example 2: Mean residence time of water in shell 1
SHELL NSHL 1 SHTHK 4.0 -
SOLUTE SELECT SEGID @PROT .AND. .NOT. HYDROGEN END -
SOLVENT SELECT SEGID W* .AND. TYPE OH2 END
CORSOL MAXSERIES 1 MAXTIMESTEPS 500 MAXATOMS 10000
ENTER AAAA SATM SHEL 1 SELECT ATOM WAT * OH2 END
TRAJECTORY FIRSTU 51 NUNIT 5
WRITE AAAA UNIT 11 DUMB TIME
* title
END
Example 3: Mean residence time histogram (alternative definition)
SHELL NSHL 1 SHTHK 4.0 -
SOLUTE SELECT SEGID @PROT .AND. .NOT. HYDROGEN END -
SOLVENT SELECT SEGID W* .AND. TYPE OH2 END
CORSOL MAXSERIES 1 MAXTIMESTEPS 500 MAXATOMS 10000
ENTER AAAA MRTI SELECT ATOM WAT * OH2 END
TRAJECTORY FIRSTU 51 NUNIT 5
WRITE AAAA UNIT 11 DUMB TIME
* title
END
Example 4: shell crossover correlation function
SHELL NSHL 2 SHTHK 4.0 -
SOLUTE SELECT SEGID @PROT .AND. .NOT. HYDROGEN END -
SOLVENT SELECT SEGID W* .AND. TYPE OH2 END
CORSOL MAXSERIES 1 MAXTIMESTEPS 500 MAXATOMS 10000
ENTER AAAA SATX SHL1 1 SHL2 2 SELECT ATOM WAT * OH2 END
TRAJECTORY FIRSTU 51 NUNIT 5
WRITE AAAA UNIT 11 DUMB TIME
* title
END
