Go to the previous, next section.
The commands described in this section are generally more simple in nature than those of previous sections. Some are perhaps obsolete, but included for the sake of completeness.
PARALLEL [CG ] [NCPU integer] [SCHED {GANG} ]
[CONGen ] [ {FREE} ]
[LOOPs ]
[OFF ]
The PARALLEL command is used to control the usr of parallel processing. Presently, parallel processing can be used for either the conformational search part of CONGEN, see section Conformational Search, or compute intensive loops in the Poisson-Boltzmann electrostatics calculations, see section Poisson-Boltzmann Electrostatics. It cannot be used for both. Parallel processing is only supported on multiprocessor Silicon Graphics workstations or servers. Parallel processing is not supported on any other machine as yet.
The options, CG or CONGEN, are used to turn parallel processing on for the conformational search. The option, LOOPS, is used to turn on parallel processing for compute intensive loops. The option, OFF, is used to turn parallel processing off. If none of these options is specified, then CONGEN searching is run in parallel.
The NCPU option is used to specify the number of CPU's to use for the calculation. If this is not specified, then the program will check the following in order:
The maximum permitted value for NCPU is the minimum of 32 and the number of CPU's on the system where CONGEN is running.
The SCHED option controls how process execution is scheduled. The option, GANG, specifies that all processes working together be scheduled as a unit. GANG is the default for compute intensive loops. The option, FREE, specifies that all processes are scheduled independently. This option is the default for conformational search.
See section Conformational Search, for more information about parallel processing in the conformational search.
If you are running a conformational search which uses Poisson-Boltzmann elecstrostatics, it is more economical to parallelizes the PBE calculation, and leave the search running serially because this optimizes memory usage. Parallel searching requires one copy of the PBE data structure per process, and this takes up a great deal of space.
For large memory jobs running in parallel on SGI workstations, it is critically important to set the STACK resource limit down from the default value. See section RLIMIT Command -- Set Resource Limits, for more information.
CODEs
The CODES command invokes the subroutine, CODES,
which determines all the parameter type code indices for the internal
coordinates and hydrogen bonds. It is useful to call this function
before invoking the CONGEN command if energy values must be
computed in a conformational search, see section Conformational Search.
DELIm char
The DELIM command sets the default command delimiter for command options which are specified as strings. The delimiter may be only one character. The default value for the delimiter is a dollar-sign, $.
DRAW derivative-factor-spec frame-spec derivative-factor-spec ::= [DFACt real] [NOMO] frame-spec ::= UNIT integer [DASH real] [FRAMe integer] [RETUrn integer]
The DRAW command (called directly from CONGEN, not to be confused with the DRAW command found under the ANALYSIS command) is useful for displaying small molecules. The output is a command file that can be read by various displaying and plotting programs such as PLT2. This command file can be edited for different types of displaying. In addition to atom positions and bonds, velocity and forces may also be displayed. The current keywords are:
{ STOP }
{ EXIT }
The STOP or EXIT commands cause the program to terminate and to ignore all command that follow this command. This is useful for making temporary modifications to input files.
DISTance
The DISTANCE command will cause the distance for every pair of atoms to be printed on a separate line. This command is not recommended for systems with more than 50 atoms. It is a great way to waste paper and there are other way to obtain this information such as with the builder commands or the analysis commands.
USER
The USER command is described in greater detail in section Interfacing to CONGEN.
TIME integer
The TIME command sets the value of TIMER in COMMON
/TIMER/ to the specified value. This variable is used to time
different functions in the program.
ENERGY, and the
times for various components of the EXEL nbonds update.
WRNLEV integer
The WRNLEV command sets the value of the WRNLEV variable in
COMMON /TIMER/ to the specified value. At the present
(17-Nov-1990) this variable is not widely used. Suggested values for
future use:
NOBOmb
The NOBOMB command prevents the program from bombing out if it hits an unrecognized command in the main program. This is useful for attempting interactive work.
DEBUg repeat(name int)
{ ALLHP }
{ ALLOC }
{ ALLSTK }
{ CGCONS }
{ CGEN }
{ CLSCHN }
{ CORE }
{ DIVZERO }
{ ESOLVE }
{ FPE }
{ GENIC }
{ GEPOL }
{ GRID }
{ GRIDSIG }
name ::= { INEXACT }
{ INVALID }
{ JCOUP }
{ MALLOC }
{ NOE }
{ OVERFLOW }
{ PARA }
{ PBE }
{ SEARCH_NEAR }
{ TLIMIT }
{ TREE }
{ UNDERFLOW }
{ XCONF }
The DEBUG command set the value for various debugging variables in the system. Although you should check the source code for the exact details, the following table gives an approximate idea of what the variables do.
cgalloc is set to -1 before being
returned.
cgalloc,
and some checks are done when memory is freed using cgfree.
cgalloc usage is checked everytime
cgalloc and cgfree are called.
stderr at the end of execution.
Note: on SGI Irix 5.3, there is a bug which prevents this code from functioning. As a result, no exceptions are trapped at all. On SGI Irix 6.0, libfpe is unavailable, so no exceptions are trapped here either. Hopefully, future releases will take care of the problem.
malloc calls on some machines
(definitely, the Iris).
WEIGHT repeat(name real) [END]
{ EB }
{ ET }
{ EP }
{ EI }
name ::= { ENB }
{ EEL }
{ EHB }
{ EC }
{ ENOE }
{ EJCP }
The WEIGHT command set the weight for each term in the potential energy function. The default value is 1.0 if no weights are specified. Since the code for the nonbonded and electrostatic terms are interdependent, these weights nust be the same. If not, the weight for the electostatic term will default to the weight for the nonbonded term.
Changes the weight of the bond energy term.
Changes the weight of the angle energy term.
Changes the weight of the torsion angle energy term.
Changes the weight of the improper torsion angle energy term.
Changes the weight of the van der Waals energy term.
Changes the weight of the electrostatic energy term.
Changes the weight of the hydrogen bond energy term.
Changes the weight of the harmonic atom and dihedral angle constraints, see section Constraints.
Changes the weight of the Nuclear Overhauser Enhancement constraints, see section NMR Constraints.
Changes the weight of the NMR J coupling constraints, see section NMR Constraints.
The GAUSSIAN command is used to invoke the Gaussian program(22) Currently, this interface may only be used to calculate partial charges for fragments of the system. It uses the Gaussian 92 program to calculate the wavefunction and electrostatic field for the fragment. Four different methods are provided for calculating partial charges from the wavefunction. All of these methods determine partial charges by performing a least squares fit of the potential generated by the partial charges to the potential calculated using the wavefunction. The fundamental difference between the methods is the layout of points where the electrostatic potential is determined by the wavefunction, and subsequently used for the least squares fit of atomic charges.
The first method, PDM, uses two programs written by Don Williams, PDM88 and PDGRID.(23)(24) The PDGRID program lays out a grid of points around the fragment where the potential will be calculated, and the PDM88 program does the least squares fit to determine the best values for the partial charges.(25) The other methods have been incorporated directly into Gaussian 92, and use different grid layouts. There is the scheme due to Merz, Singh, and Kollman,(26)(27) identified by the keyword, MK; the scheme due to Chirlian and Francl,(28) identified by the keyword, CHELP; and the scheme to Breneman and Wiberg,(29) identified by the keyword, CHELPG.
All of these schemes have their own values for van der Waals radii encoded within them. However, the default in this interface is to use the radii from the parameters in CONGEN. If you want to use the radii in the external programs, use the EXTRADII keyword.
This command simplifies the use of these three programs. You specify the atoms you want charges for, and the programs are invoked in turn to calculate the charges. Remember that the time for the calculation increases approximately with the fourth power of the number of electrons. A number of files are generated when this command is executed. Normally, these files are deleted after the command is complete, but you can request that they be saved.
Note that the collection of atoms that you specify should be a complete molecule including hydrogens. It does not make physical sense to do anything different, although the program does not check for completeness.
If you use this command to calculate results that are eventually published, please ensure that both Gaussian 92 and the fitting scheme you use is properly referenced.
GAUSsian CHARges {SELECT atom-selection END}
[BASIs word] [SCF word] [TOTAl real] [MEMOry int]
[UNIT unit] [PREFix word] [EXTRadii] [DIPOle]
[PDM [UNDEr real] [SHELl real] [SPACing real] ]
[MK ]
[CHELP ]
[CHELPG ]
[STEPs repeat(step-options) END]
[SAVE] [NORUn]
[MERGe atom-selection END]
repeat( AVERage atom-selection END )
[ ALL ]
[ NONE ]
[ [NO]CREAte ]
[ [NO]HF ]
step-option ::= [ [NO]GRID ]
[ [NO]POTEntial ]
[ [NO]FIT ]
[ [NO]SCAN ]
[ [NO]DELEte ]
See section Atom Selection, for the syntax of an atom-selection.
The GAUSSIAN command functions by writing a set of input files for Gaussian, PDGRID, and PDM88; preparing a Bourne shell script to execute each program in turn; executing the script; and reading the results. The options are interpreted as follows:
The following table gives the file types for all the intermediate files used:
The TEST command is used to test internal operations within CONGEN. Currently, three test operations are provided; energy derivatives, calculation of maximum contact distances for the VAVOID sidechain option when the hydrogen bond energy replaces the van der Waals energy, and calculation of torsion angle minima.
TEST [DERIV [DELTA real] [CUT real]]
[VAHB [MAXEVDW real]]
[PHIMIN [SGRID real] [SYMMETRY int]]
The energy derivative test is invoked by the DERIV keyword. The code works by computing numerical derivatives of energy as shown: and comparing them against the analytic derivatives computed by the code. Statistics of the differences are calculated and a histogram of the differences is displayed.
The keyword, DELTA, specifies the value of h in the above expression. The default value is 0.001. For single precision arithmetic, this value is close to optimum.(30) The keyword, CUT, specifies a printing cutoff. Any difference in derivative whose magnitude exceeds this value will be individually displayed.
The VAVOID hydrogen bond test checks the calculation of maximum distance for a given value of MAXEVDW for the hydrogen bond potential. It is invoked using the VAHB keyword. It performs the calculation for all hydrogen bond parameters and shows the distance along with the calculated energy at that distance. The keyword, MAXEVDW, is used to set a value for the cutoff energy. The default value is 20 kcal/mole.
The torsion energy minimum test is designed to check the code which finds torsion angle values to use when performing a sidechain degree of freedom in a conformational search, see section Sidechain Degree of Freedom. In order to see the effect of this test, the CGEN debug variable, see section Set Debugging Variables -- DEBUG, must be set to 2 or larger. The SYMMETRY keyword specifies the rotational symmetry for the clump and defaults to 1. The SGRID keyword specifies the sidechain grid to use. A value of -1 means use the minimum energy periodicity. Positive values are interpreted as the grid in degrees. The default is -1.
The GEPOL command is used to set defaults for GEPOL surface calculations(31) in the analysis facility. See section Static Properties of Atoms, for more information about the GEPOL surfaces.
There is also an experimental capability to invoke the GEPOL_INCR subroutine using the RUN option.
GEPOL [NDIV int] [OFAC real] [RMIN real]
[RSOL real] [RGRI real] [CAVIty real] [[NO]BULK]
[RUN run-options]
run-options ::= [WSURF] {INIT } [PEER <UNIT>] [PROP <UNIT>]
[ASURF] {PUSH atom-selection}
[ESURF] {POP }
The options in the GEPOL command control parameters used by the GEPOL algorithm.(32)(33)(34) They have the following interpretation:
OFAC and RMIN are the parameters that control the creation of new spheres.
The RUN keyword specifies that the GEPOL_INCR subroutine is to be run. The keywords; WSURF, ASURF, and ESURF; specify van der Waals, accessible, and molecular surfaces, respectively. The keywords; INIT, PUSH, and POP; specify initialization, pushing the selected set of atoms, and popping the last set of atoms, respectively. The PEER keyword specifies a unit where all the spheres will be written as input to the peer program, see section peer -- Interactive Molecular Display Program. The PROP keyword specifies a unit where the atomic surfaces will be written as a property table suitable for use in the Analysis Facility, see section Table Input and Output.
The RLIMIT command is used to set and display computer resource limits. It is critically important to set the stacksize limit (STACK) when running very large calculations in parallel on an SGI workstation. The command is only implemented on a SGI system.
RLIMIT repeat(limit [int ])
[INFinity]
[CORE ]
[CPU ]
[DATA ]
limit ::= [FSIZE ]
[NOFILE]
[STACK ]
[VMEM ]
[RSS ]
The options in the RLIMIT command set computer resource limits. After the command finishes execution, the current limits are printed. The keywords have the following meaning:
The SHELL executes a command under the Bourne shell for Unix systems, or under DCL for VMS systems. The syntax is
SHELL string
where string is the command to be executed.
Go to the previous, next section.