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Analysis Commands

The ANALysis command is an energy and structure analysis facility that has been developed to examine both static and dynamic properties. The current code allows energy partition analysis and energy contribution analysis from free energy simulations. It also can produce a detailed printout of structural and energy term contributions for selected atoms

Description of the ANALysis Command

Syntax:

ANALys { ON                                                         }
       { TERM  { [ALL] }  { NONBond     } [UNIT int] atom-selection }
       {       {  ANY  }  { [NONOnbond] }                           }
       { OFF                                                        }


ON    Enable energy partition analysis and disable FAST routines.

OFF   Disable analysis and restore FAST option defaults.

TERM  Setup energy term print data and disable FAST routines.

ALL (default)       Print energy terms involving only selected atoms
ANY                 Print energy terms when any of the atoms is selected

NONBond             In addition to internal terms, also print nonbond terms
NONOnbond (default) Do not print electrostatic and vdw energy data

UNIT integer        Write the energy term printout data to a formatted file
                    Otherwise, write data to the output file.

Energy term option of the ANALysis Command

The ANALysis ON command enables energy partition analysis and disables the FAST routines. This will slow the calculation (especially on vector machines), but allows a detailed, atom by atom, energy analysis. Everytime the energy routine is invoked, the energy for each atom is stored in the ECONT array. During PERT dynamics, the EPCONT is filled with the time average energy difference on a atom by atom basis including every step of dynamics. This allows the free energy differences to be analyzed based on atom contributions.

The energy partition array can be accessed with the SCALar ECONt commands. Econt. The sum of all of the elements of the ECONT array is usually the total energy, but some energy terms, such as extended electrostatics, will not be included. The command:

SCALar ECONT STATistics

can be used to check the total energy and the command

SCALar EPCONT ....

can be used to examine atom contributions to energy differences for PERT.

The ANALysis TERM command will cause all selected energy terms to be printed to the specified output unit (default: standard CHARMM output). The ALL keyword (default) will list elements where all atoms are selected. The ANY keyword will cause terms including any selected atom to be listed. The NONOnbond keyword (default) suppresses the listing of vdw and electrostatic energy terms. The NONBonded keywords also allows the analysis of vdw and electrostatic interactions.

The ANALys OFF command enables the FAST routines and disables the resetting of the ECONT array (i.e. the ECONT array will not change, but may still be accessed. This command also disables the energy term analysis.