Analysis Commands In CHARMM23, new analysis commands are under development, but some features are currently functional. * Menu: * Description:: Description of analysis facility * Energy:: Energy partitioning
Description of the ANALysis Command ANALys {ON } Enable analysis and disable FAST routines. {OFF} Disable analysis and restore FAST option defaults. The ANALysis command is a new energy and structure table facility that is being developed to examine both static and dynamic properties. The current code only allows energy partition analysis and energy contribution analysis from free energy simulations. It also can produce a detailed printout of energy term contributions.
Energy option of the ANALysis Command Syntax: ANALys { ON } { TERM { [ALL] } { NONBond } [UNIT int] atom-selection } { { ANY } { [NONOnbond] } } { OFF } The ANALysis ON command enables energy partition analysis and disables the FAST routines. This will slow the calculation (especially on vector machines), but allow 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 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. The energy partition array can be accessed with the SCALar ECONt commands. *note Econt:(scalar.doc). 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.
NIH/DCRT/Laboratory for Structural Biology
FDA/CBER/OVRR Biophysics Laboratory