scalar (c41b2)
SCALar : commands to manipulate scalar atom properties
[SYNTAX SCALar]
SCALar keyname { } [atom-selection]
{ = keyname } ! A = B
{ COPY keyname } ! A = B
{ SUM keyname } ! A = A + B
{ PROD keyname } ! A = A * B
{ SET <real> } ! A = <real>
{ ADD <real> } ! A = <real> + A
{ MULT <real> } ! A = <real> * A
{ DIVI <real> } ! A = A / <real>
{ SIGN } ! A = sign ( A )
{ INTEger } ! A = int ( A )
{ RECIprocal } ! A = 1/ A
{ LOG } ! A = ln ( A )
{ EXP } ! A = exp ( A )
{ ABS } ! A = ABS ( A )
{ NORM } ! A = A / 2-norm(A)
{ MIN <real> } ! A = MIN (A,<real>)
{ MAX <real> } ! A = MAX(A,<real>)
{ POWEr <real> } ! A = A ** <real>
{ POW2r } ! A = A * A
{ IPOW <real> } ! A = A ** int(<real>), OK for neg A
{ SQRT } ! A = SQRT(A)
{ RANDom } ! A = random
{ HBCOunt } ! A = #of hbonds
{ SHOW [SORT] }
{ STATistics weight_opt }
{ STORe store_number } ! S(i) = A(i)
{ RECAll store_number } ! A(i) = S(i)
{ +STOre store_number } ! S(i) = S(i) + A(i)
{ *STOre store_number } ! S(i) = S(i) * A(i)
{ READ <unit> }
{ [H]WRITe <unit> }
{ }
{ [ ALL ] }
{ AVERage [ BYSEgment ] } ! S(i) = sum(S(j))/Nj
{ [ BYREsidue ] } ! averaged over each selected
{ [ BYGRoup ] } ! atom of each item
weight_opt
store_number ::= any number between 1 and 9. store_number
weight_opt ::= [ WEIGht store_number ] [MASS]
keyname ::= { X }
{ Y } ! main coordinates
{ Z }
{ WMAIn } ! main coordinate weights
{ XCOMp }
{ YCOMp } ! comparison coordinates
{ ZCOMp }
{ WCOMp } ! comparison coordinate weights
{ DX psf_no } ! forces from last energy eval
{ DY psf_no } ! or force difference from last EPERT
{ DZ psf_no } ! eval when using PSF 0
{ ECONt } ! Energy partition array
{ EPCOnt } ! Free energy difference atom partition
{ MASS psf_no } ! atom masses
{ CHARge psf_no } ! atom charges
{ CONStraints psf_no } ! harmonic constraint constants
{ XREF psf_no }
{ YREF psf_no } ! reference coordinates
{ ZREF psf_no }
{ FBETa } ! friction coefficients
{ MOVE psf_no } ! rigid constraints flag
{ TYPE psf_no } ! atom chemical type codes
{ IGNOre } ! ASP flag for ignoring atoms
{ ASPValue } ! ASP parameter value
{ VDWSurface } ! ASP van der Waals surface
{ RSCAle psf_no } ! Radius scale facor for vdw
{ WCAD psf_no } ! scale facor for WCA potential
{ ALPHa (**) psf_no } ! atom polarizability
{ EFFEct (**) psf_no } ! effective number of electrons
{ RADIus (**) psf_no } ! van der Waal radii
{ FQPRin (**) } ! FlucQ principal quantum number
{ FQZeta (**) } ! FlucQ Slater orbital exponent
{ FQCHi (**) } ! FlucQ electronegativity parameter
{ FQMAss (**) } ! FlucQ charge mass
{ FQJZ (**) } ! FlucQ self-interaction
{ FQCForce } ! FlucQ charge force
{ FQOLd } ! FlucQ charges from last timestep
{ SCAx (x::=1,2,..,9)} ! specific scalar store array
{ ONE (**) } ! vector with all 1's
{ ZERO (**) } ! vector with all 0's
{ VARC } ! Offset for the Variable LJ cutoffs
{ SGWT } ! Self-guiding weights for SGLD simulation
psf_no::= { PSF 0 } ! which PSF (use only with PERT)
{ [PSF 1] }
(**) = For the keynames labeled (**), the array values may not
be modified by any scalar command, but they may be used in the
SHOW, STORe, STATistics, or as any second keyname (e.g. COPY).
In order to change the "ALPHa", "EFFEct", or "RADIus" value, one must
change the atom's "TYPE" value, which in turn determines these values.
All of the SCALar commands allow an atom selection.
The dimension of all vectors is equal to the number of atoms. (see the
vibrational analysis section for 3N vector manipulations).
The READ option reads from an ascii file all selected entries,
one value per line. This file should have a valid value within the first
40 characters of each line, and should not have a CHARMM title.
The [H]WRIT option writes all selected entries to an ascii file,
one item per line for WRITe or all on one line (Horizontally) for HWRIte.
The STATistics and AVERage options accept a weighting option. If
not specified, all atoms will have an equal weighting. If specified, the
weighting of each atom will be in the specified stored vector. For the
AVERage option, the averaging may be done over ALL selected atoms, or over
groups of selected atoms defined be segment, residue, or group boundaries.
For example if one wants to print out the rms mass weighted
fluctutions for the sidechain of each residue, the sequence should
be something like;
COOR DYNA .... ! put the rms fluctuations in the weighting array
SCALar MASS STORe 1 ! put the masses in the first storage vector
SCALar WMAIn IPOW 2 ! convert rms fluctuation to mean squared fluctuations.
SCALar WMAIn AVERage BYREsidue WEIGht 1 SELE .NOT.
( TYPE CA .OR. TYPE C .OR. TYPE N .OR. TYPE H .OR. TYPE O ) END
! does the averaging for the sidechain with mass weighting
SCALar WMAIn SQRT ! take root to get rms of square fluctuation data.
SCALar WMAIn SHOW SELE TYPE CB END ! show the results for each residue
Note: to get the mass weighted average rms fluctuations, remove steps 3 and 5.
The RANDom option sets a different random number for each selected
atom based on the specifications given in the RANDom command
(» random .).
NOTE: Variable length LJ interactions are now activitaed first by a CHARMM
command: varcut on. This turns on a logical making the varcut scalar arrays
accessible. The arrays are deallocated and the logical turned off with
the command: varcut off. Use of the scalar varc manipulations w/o first turning
varcut on now prints a warning message and nothing is done. clb3, 03/2011.
Example on how to use the Variable Lennard-Jones Cutoff Method (VLJCM).
VLJCM allows the user to apply different length lennard-jones cutoff's to
different atoms in the system. This is useful when using force-fields which
are parameterized for a specific LJ cutoff distance (eg EEF1) and one wants
to introduce new types of molecules which need larger LJ cutoffs. In this
situation VLJCM allows the user to keep the original LJ cutoff for a certain
set of atoms in the system, and apply a different LJ cutoff to different
atoms in the system. Here is an example of how to set up VLJCM before
dynamics is run. Assume you have a binary mixture of atoms labeled A and B:
! The nonbonded options below are part of the model
update ctonnb 7. ctofnb 9. cutnb @cutnb cutim @cutim group rdie
! scale nonbond interactions
scalar varc set 10.0 sele resname A end
scalar varc show
In the above example the default LJ cutoff is 9 angstroms and the switching
region starts at 7 angstroms. We set up VLJCM using the 'scalar varc' command.
In this case the new LJ cutoff will be computed based on the 10.0 angstrom
arguement supplied.
If there is a B-B LJ interaction the default LJ cutoff is applied. If there is
an A-A LJ interaction the default LJ cutoff is computed as follows:
ctonnb=(varc(A)+varc(A))/2
ctofnb=(varc(A)+varc(A))/2 + cdiff
where 'varc(A)' = 10.0 angstroms, and 'cdiff' = 2 angstroms (taken from the
default size of the switching region). Thus for A-A LJ interactions ctonnb=10.
ctofnb=12.
In the case of A-B interactions we have 'varc(A)' = 10.0 angstroms and
'varc(B)' = 0.0 angstroms, which leads to ctonnb=5. ctofnb=7.
[SYNTAX SCALar]
SCALar keyname { } [atom-selection]
{ = keyname } ! A = B
{ COPY keyname } ! A = B
{ SUM keyname } ! A = A + B
{ PROD keyname } ! A = A * B
{ SET <real> } ! A = <real>
{ ADD <real> } ! A = <real> + A
{ MULT <real> } ! A = <real> * A
{ DIVI <real> } ! A = A / <real>
{ SIGN } ! A = sign ( A )
{ INTEger } ! A = int ( A )
{ RECIprocal } ! A = 1/ A
{ LOG } ! A = ln ( A )
{ EXP } ! A = exp ( A )
{ ABS } ! A = ABS ( A )
{ NORM } ! A = A / 2-norm(A)
{ MIN <real> } ! A = MIN (A,<real>)
{ MAX <real> } ! A = MAX(A,<real>)
{ POWEr <real> } ! A = A ** <real>
{ POW2r } ! A = A * A
{ IPOW <real> } ! A = A ** int(<real>), OK for neg A
{ SQRT } ! A = SQRT(A)
{ RANDom } ! A = random
{ HBCOunt } ! A = #of hbonds
{ SHOW [SORT] }
{ STATistics weight_opt }
{ STORe store_number } ! S(i) = A(i)
{ RECAll store_number } ! A(i) = S(i)
{ +STOre store_number } ! S(i) = S(i) + A(i)
{ *STOre store_number } ! S(i) = S(i) * A(i)
{ READ <unit> }
{ [H]WRITe <unit> }
{ }
{ [ ALL ] }
{ AVERage [ BYSEgment ] } ! S(i) = sum(S(j))/Nj
{ [ BYREsidue ] } ! averaged over each selected
{ [ BYGRoup ] } ! atom of each item
weight_opt
store_number ::= any number between 1 and 9. store_number
weight_opt ::= [ WEIGht store_number ] [MASS]
keyname ::= { X }
{ Y } ! main coordinates
{ Z }
{ WMAIn } ! main coordinate weights
{ XCOMp }
{ YCOMp } ! comparison coordinates
{ ZCOMp }
{ WCOMp } ! comparison coordinate weights
{ DX psf_no } ! forces from last energy eval
{ DY psf_no } ! or force difference from last EPERT
{ DZ psf_no } ! eval when using PSF 0
{ ECONt } ! Energy partition array
{ EPCOnt } ! Free energy difference atom partition
{ MASS psf_no } ! atom masses
{ CHARge psf_no } ! atom charges
{ CONStraints psf_no } ! harmonic constraint constants
{ XREF psf_no }
{ YREF psf_no } ! reference coordinates
{ ZREF psf_no }
{ FBETa } ! friction coefficients
{ MOVE psf_no } ! rigid constraints flag
{ TYPE psf_no } ! atom chemical type codes
{ IGNOre } ! ASP flag for ignoring atoms
{ ASPValue } ! ASP parameter value
{ VDWSurface } ! ASP van der Waals surface
{ RSCAle psf_no } ! Radius scale facor for vdw
{ WCAD psf_no } ! scale facor for WCA potential
{ ALPHa (**) psf_no } ! atom polarizability
{ EFFEct (**) psf_no } ! effective number of electrons
{ RADIus (**) psf_no } ! van der Waal radii
{ FQPRin (**) } ! FlucQ principal quantum number
{ FQZeta (**) } ! FlucQ Slater orbital exponent
{ FQCHi (**) } ! FlucQ electronegativity parameter
{ FQMAss (**) } ! FlucQ charge mass
{ FQJZ (**) } ! FlucQ self-interaction
{ FQCForce } ! FlucQ charge force
{ FQOLd } ! FlucQ charges from last timestep
{ SCAx (x::=1,2,..,9)} ! specific scalar store array
{ ONE (**) } ! vector with all 1's
{ ZERO (**) } ! vector with all 0's
{ VARC } ! Offset for the Variable LJ cutoffs
{ SGWT } ! Self-guiding weights for SGLD simulation
psf_no::= { PSF 0 } ! which PSF (use only with PERT)
{ [PSF 1] }
(**) = For the keynames labeled (**), the array values may not
be modified by any scalar command, but they may be used in the
SHOW, STORe, STATistics, or as any second keyname (e.g. COPY).
In order to change the "ALPHa", "EFFEct", or "RADIus" value, one must
change the atom's "TYPE" value, which in turn determines these values.
All of the SCALar commands allow an atom selection.
The dimension of all vectors is equal to the number of atoms. (see the
vibrational analysis section for 3N vector manipulations).
The READ option reads from an ascii file all selected entries,
one value per line. This file should have a valid value within the first
40 characters of each line, and should not have a CHARMM title.
The [H]WRIT option writes all selected entries to an ascii file,
one item per line for WRITe or all on one line (Horizontally) for HWRIte.
The STATistics and AVERage options accept a weighting option. If
not specified, all atoms will have an equal weighting. If specified, the
weighting of each atom will be in the specified stored vector. For the
AVERage option, the averaging may be done over ALL selected atoms, or over
groups of selected atoms defined be segment, residue, or group boundaries.
For example if one wants to print out the rms mass weighted
fluctutions for the sidechain of each residue, the sequence should
be something like;
COOR DYNA .... ! put the rms fluctuations in the weighting array
SCALar MASS STORe 1 ! put the masses in the first storage vector
SCALar WMAIn IPOW 2 ! convert rms fluctuation to mean squared fluctuations.
SCALar WMAIn AVERage BYREsidue WEIGht 1 SELE .NOT.
( TYPE CA .OR. TYPE C .OR. TYPE N .OR. TYPE H .OR. TYPE O ) END
! does the averaging for the sidechain with mass weighting
SCALar WMAIn SQRT ! take root to get rms of square fluctuation data.
SCALar WMAIn SHOW SELE TYPE CB END ! show the results for each residue
Note: to get the mass weighted average rms fluctuations, remove steps 3 and 5.
The RANDom option sets a different random number for each selected
atom based on the specifications given in the RANDom command
(» random .).
NOTE: Variable length LJ interactions are now activitaed first by a CHARMM
command: varcut on. This turns on a logical making the varcut scalar arrays
accessible. The arrays are deallocated and the logical turned off with
the command: varcut off. Use of the scalar varc manipulations w/o first turning
varcut on now prints a warning message and nothing is done. clb3, 03/2011.
Example on how to use the Variable Lennard-Jones Cutoff Method (VLJCM).
VLJCM allows the user to apply different length lennard-jones cutoff's to
different atoms in the system. This is useful when using force-fields which
are parameterized for a specific LJ cutoff distance (eg EEF1) and one wants
to introduce new types of molecules which need larger LJ cutoffs. In this
situation VLJCM allows the user to keep the original LJ cutoff for a certain
set of atoms in the system, and apply a different LJ cutoff to different
atoms in the system. Here is an example of how to set up VLJCM before
dynamics is run. Assume you have a binary mixture of atoms labeled A and B:
! The nonbonded options below are part of the model
update ctonnb 7. ctofnb 9. cutnb @cutnb cutim @cutim group rdie
! scale nonbond interactions
scalar varc set 10.0 sele resname A end
scalar varc show
In the above example the default LJ cutoff is 9 angstroms and the switching
region starts at 7 angstroms. We set up VLJCM using the 'scalar varc' command.
In this case the new LJ cutoff will be computed based on the 10.0 angstrom
arguement supplied.
If there is a B-B LJ interaction the default LJ cutoff is applied. If there is
an A-A LJ interaction the default LJ cutoff is computed as follows:
ctonnb=(varc(A)+varc(A))/2
ctofnb=(varc(A)+varc(A))/2 + cdiff
where 'varc(A)' = 10.0 angstroms, and 'cdiff' = 2 angstroms (taken from the
default size of the switching region). Thus for A-A LJ interactions ctonnb=10.
ctofnb=12.
In the case of A-B interactions we have 'varc(A)' = 10.0 angstroms and
'varc(B)' = 0.0 angstroms, which leads to ctonnb=5. ctofnb=7.